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03_run_data_processing.R
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source("02_process_data.R")
compile_tcc_counts(base_dir="/home/Shared_taupo/data/seq/conquer/database/data-tcc/SRP073808",
mae_dir="/home/Shared_taupo/data/seq/conquer/database/data-mae/",
out_dir="/home/Shared_taupo/data/seq/conquer/database/data-tcc",
experiment_id="SRP073808", verbose=TRUE)
compile_tcc_counts(base_dir="/home/Shared_taupo/data/seq/conquer/database/data-tcc/GSE52529-GPL16791",
mae_dir="/home/Shared_taupo/data/seq/conquer/database/data-mae/",
out_dir="/home/Shared_taupo/data/seq/conquer/database/data-tcc",
experiment_id="GSE52529-GPL16791", verbose=TRUE)
compile_tcc_counts(base_dir="/home/Shared_taupo/data/seq/conquer/database/data-tcc/GSE60749-GPL13112",
mae_dir="/home/Shared_taupo/data/seq/conquer/database/data-mae/",
out_dir="/home/Shared_taupo/data/seq/conquer/database/data-tcc",
experiment_id="GSE60749-GPL13112", verbose=TRUE)
#salmonbin <- "/usr/local/software/SalmonBeta-0.6.1_DebianSqueeze/bin/salmon"
#salmonbin <- "software/Salmon-0.7.2_linux_x86_64/bin/salmon"
salmonbin <- "/home/charlotte/software/Salmon-0.8.2_linux_x86_64/bin/salmon"
kallistobin <- "/usr/local/software/kallisto_linux-v0.44.0/kallisto"
rapmapbin <- "/home/charlotte/software/RapMap/bin/rapmap"
fastqcbin <- "FastQC_v0.11.6.devel/fastqc"
cutadaptbin <- "/home/charlotte/miniconda3/bin/cutadapt"
#multiqcbin <- "/home/charlotte/miniconda2/bin/multiqc"
multiqcbin <- "/home/charlotte/miniconda3/bin/multiqc"
Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap <-
readRDS("reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap.rds")
Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap <-
readRDS("reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap.rds")
Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.txgenemap <-
readRDS("reference-files/danio-rerio/Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.txgenemap.rds")
Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges <-
readRDS("reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges.rds")
Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges <-
readRDS("reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges.rds")
Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.granges <-
readRDS("reference-files/danio-rerio/Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.granges.rds")
adapterseq <- "AGATCGGAAGAGC"
#adapterseq <- "file:adapters.fa"
source("02_process_data.R")
## SRP073808 - TCC
process_data(id = "SRP073808", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 27996962, shortname = "Koh2016",
datalink = "https://www.ncbi.nlm.nih.gov/sra?term=SRP073808",
description = "in vitro cultured H7 embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.8.2.sidx",
kallistobin = kallistobin,
kallistoindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.44.kidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "Run", groupid = "LibraryName",
geodata = FALSE, phenofile = "data-raw/SRP073808/SRP073808_pheno.txt",
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("tcc"), verbose = TRUE,
force = FALSE)
## GSE52529-GPL16791
process_data(id = "GSE52529-GPL16791", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 24658644, shortname = "Trapnell2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52529",
description = "primary myoblasts over a time course of serum-induced differentiation",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.6.1.sidx",
kallistobin = kallistobin,
kallistoindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.44.kidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("tcc"), verbose = TRUE,
force = FALSE)
## GSE60749, HiSeq2000 (25bp reads) - TCC
process_data(id = "GSE60749-GPL13112", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 25471879, shortname = "Kumar2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60749",
description = "mESCs with various genetic perturbations, cultured in different media",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.6.1.sidx",
kallistobin = kallistobin,
kallistoindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.44.kidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("source_name_ch1", "characteristics_ch1.1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("tcc"), verbose=TRUE,
force = FALSE)
## GSE84465
process_data(id = "GSE84465", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 29091775, shortname = "Darmanis2017",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84465",
description = "glioblastoma tumors",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("description", "neoplastic.ch1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 2, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## Running
## GSE81903
process_data(id = "GSE81903", dtype = "fl", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 27565351, shortname = "Shekhar2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81903",
description = "P17 retinal cells from the Kcng4-cre;stop-YFP X Thy1-stop-YFP Line#1 mice",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.2",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE80232
process_data(id = "GSE80232", dtype = "fl", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 27565351, shortname = "Shekhar2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80232",
description = "P17 retinal cells from the Tg(Chx10-EGFP/cre,-ALPP)2Clc or Vsx2-GFP transgenic line",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("source_name_ch1", "characteristics_ch1.1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE80032
process_data(id = "GSE80032", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 27923766, shortname = "Wollny2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80032",
description = "heterogeneity of acinar cells",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE94383
process_data(id = "GSE94383", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 28396000, shortname = "Lane2017",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94383",
description = "LPS stimulated and unstimulated 264.7 cells",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("characteristics_ch1.1", "characteristics_ch1.2"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE79102
process_data(id = "GSE79102", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 28346451, shortname = "Kiselev2017",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79102",
description = "different patients with myeloproloferative disease",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 2, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## To run
## GSE102299-smartseq2
process_data(id = "GSE102299-smartseq2", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 28902842, shortname = "Wallrapp2017",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102299",
description = "innate lymphoid cells from mouse lungs after various treatments",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.4",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE81076-GPL16791
process_data(id = "GSE81076-GPL16791", dtype = "umi", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 27345837, shortname = "Grun2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81076",
description = "pancreatic cells from donors with and without type 2 diabetes",
protocol = "CEL-Seq", protocoltype = "UMI",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin, salmonindex = NULL, libtype = NULL, bias = FALSE,
rapmapbin = rapmapbin,
rapmapindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.k15.0.5.0.ridx",
umis_transform = "software/umis/examples/CEL-Seq/transform.json",
cell_barcodes = "data-raw/GSE81076-GPL16791/GSE81076_cel-seq_barcodes.txt",
sncol = "SampleName", groupid = "characteristics_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "umis", "multiqc", "mae", "scater"),
force = FALSE)
## GSE81076-GPL18573
process_data(id = "GSE81076-GPL18573", dtype = "umi", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 27345837, shortname = "Grun2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81076",
description = "pancreatic cells from donors with and without type 2 diabetes",
protocol = "CEL-Seq", protocoltype = "UMI",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin, salmonindex = NULL, libtype = NULL, bias = FALSE,
rapmapbin = rapmapbin,
rapmapindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.k15.0.5.0.ridx",
umis_transform = "software/umis/examples/CEL-Seq/transform.json",
cell_barcodes = "data-raw/GSE81076-GPL18573/GSE81076_cel-seq_barcodes.txt",
sncol = "SampleName", groupid = "characteristics_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "umis", "multiqc", "mae", "scater"),
force = FALSE)
## GSE100911
process_data(id = "GSE100911", dtype = "fl", rtype = "paired",
organism = "Danio rerio", genome = "GRCz10.87",
pmid = "", shortname = "Tang2017",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100911",
description = "hematopoietic and renal cell heterogeneity",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/danio-rerio/Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.1",
geodata = TRUE, phenofile = NULL,
gene_granges = Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Danio_rerio.GRCz10.87.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## Not single cells
## GSE97142
process_data(id = "GSE97142", dtype = "umi", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 28536247, shortname = "Dierickx2017",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97142",
description = "", protocol = "", protocoltype = "",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin, salmonindex = NULL, libtype = NULL, bias = FALSE,
rapmapbin = rapmapbin,
rapmapindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.k15.0.5.0.ridx",
umis_transform = "software/umis/examples/CEL-Seq/transform.json",
cell_barcodes = "data-raw/GSE97142/GSE97142_cel-seq_barcodes.txt",
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "umis", "multiqc", "mae", "scater"),
force = FALSE)
## GSE71982
process_data(id = "GSE71982", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 26469390, shortname = "Burns2015",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71982",
description = "utricular and cochlear sensory epithelia of newborn mice",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("source_name_ch1", "characteristics_ch1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE64016
process_data(id = "GSE64016", dtype = "fl", rtype = "single",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 26301841, shortname = "Leng2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64016",
description = "H1 and H1-Fucci cells",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 2, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE66053-GPL18573
process_data(id = "GSE66053-GPL18573", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 25866248, shortname = "PadovanMerhar2015",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66053",
description = "live and fixed single cells",
protocol = "Fluidigm C1 Auto prep", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.k15.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## SRP073808
process_data(id = "SRP073808", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 27996962, shortname = "Koh2016",
datalink = "https://www.ncbi.nlm.nih.gov/sra?term=SRP073808",
description = "in vitro cultured H7 embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "Run", groupid = "LibraryName",
geodata = FALSE, phenofile = "data-raw/SRP073808/SRP073808_pheno.txt",
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE52583-GPL16417
process_data(id = "GSE52583-GPL16417", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 24739965, shortname = "Treutlein2014",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52583",
description = "lung epithelial cells at different developmental stages",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.2",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE52583-GPL13112
process_data(id = "GSE52583-GPL13112", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 24739965, shortname = "Treutlein2014",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52583",
description = "lung epithelial cells at different developmental stages",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.2",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE62270-GPL19057
process_data(id = "GSE62270-GPL19057", dtype = "umi", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 26287467, shortname = "Grun2015",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62270",
description = "cells from mouse intestinal organoids",
protocol = "CEL-Seq", protocoltype = "UMI",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin, salmonindex = NULL, libtype = NULL, bias = FALSE,
rapmapbin = rapmapbin,
rapmapindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.5.0.ridx",
umis_transform = "software/umis/examples/CEL-Seq/transform.json",
cell_barcodes = "data-raw/GSE62270-GPL19057/GSE62270_96BC.txt",
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "umis", "multiqc", "mae", "scater"),
force = FALSE)
## GSE62270-GPL17021
process_data(id = "GSE62270-GPL17021", dtype = "umi", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 26287467, shortname = "Grun2015",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62270",
description = "cells from mouse intestinal organoids",
protocol = "CEL-Seq", protocoltype = "UMI",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin, salmonindex = NULL, libtype = NULL, bias = FALSE,
rapmapbin = rapmapbin,
rapmapindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.5.0.ridx",
umis_transform = "software/umis/examples/CEL-Seq/transform.json",
cell_barcodes = "data-raw/GSE62270-GPL17021/GSE62270_96BC.txt",
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "umis", "multiqc", "mae", "scater"),
force = FALSE)
## GSE78779-GPL17021
process_data(id = "GSE78779-GPL17021", dtype = "umi", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 27121950, shortname = "Hashimshony2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78779",
description = "dendritic and fibroblast cells analyzed with different protocols",
protocol = "CEL-Seq/CEL-Seq2/Smart-Seq", protocoltype = "UMI",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin, salmonindex = NULL, libtype = NULL, bias = FALSE,
rapmapbin = rapmapbin,
rapmapindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.5.0.ridx",
umis_transform = "software/umis/examples/CEL-Seq2/transform.json",
cell_barcodes = NULL,
sncol = "SampleName", groupid = c("source_name_ch1", "description"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "umis", "multiqc", "mae", "scater"),
force = FALSE)
## E-MTAB-3929
process_data(id = "EMTAB3929", dtype = "fl", rtype = "single",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 27062923, shortname = "Petropoulos2016",
datalink = "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3929/",
description = "preimplantation embryos from embryonic day 3 to 7",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.8.2.sidx",
libtype = "A", bias = TRUE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "LibraryName",
groupid = c("Characteristics.developmental.stage.", "Characteristics.treatment."),
geodata = FALSE, phenofile = "data-raw/EMTAB3929/EMTAB3929_pheno.txt",
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE66507
process_data(id = "GSE66507", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 26293300, shortname = "Blakeley2015",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66507",
description = "preimplantation embryos",
protocol = "SMARTer", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.7.2.sidx",
libtype = "A", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE71585, HiSeq2000
process_data(id = "GSE71585-GPL13112", dtype = "fl", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 26727548, shortname = "Tasic2016",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585",
description = "cell type identification in primary visual cortex",
protocol = "SMARTer", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.7.2.sidx",
libtype = "A", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE71585, HiSeq2500
process_data(id = "GSE71585-GPL17021", dtype = "fl", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 26727548, shortname = "Tasic2016",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585",
description = "cell type identification in primary visual cortex",
protocol = "SMARTer", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.7.2.sidx",
libtype = "A", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1.1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## E-MTAB-2805
process_data(id = "EMTAB2805", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 25599176, shortname = "Buettner2015",
datalink = "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2805/",
description = "mESC in different cell cycle stages",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "LibraryName", groupid = "cell_cycle_stage",
geodata = FALSE, phenofile = "data-raw/EMTAB2805/EMTAB2805_pheno.txt",
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE77847
process_data(id = "GSE77847", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 27016502, shortname = "Meyer2016",
datalink = "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77847",
description = "Dnmt3a loss of function in Flt3-ITD and Dnmt3a-mutant AML",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "characteristics_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE44183human
process_data(id = "GSE44183-GPL11154", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 23892778, shortname = "Xue2013",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183",
description = "embryonal development from oocyte to morula",
protocol = "Tang2010", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "Sample_Name_s", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE44183mouse
process_data(id = "GSE44183-GPL13112", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 23892778, shortname = "Xue2013",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183",
description = "embryonal development from oocyte to morula",
protocol = "Tang2010", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "Sample_Name_s", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE44183mouse, trimmed
process_data(id = "GSE44183-GPL13112-trimmed", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 23892778, shortname = "Xue2013",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183",
description = "embryonal development from oocyte to morula",
protocol = "Tang2010", protocoltype = "full-length",
dotrim = TRUE, cutadaptbin = cutadaptbin, adapterseq = "AGATCGGAAGAGC",
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "Sample_Name_s", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE45719
process_data(id = "GSE45719", dtype = "fl", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 24408435, shortname = "Deng2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719",
description = "development from zygote to blastocyst + adult liver",
protocol = "SMART-Seq", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "U", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE74596
process_data(id = "GSE74596", dtype = "fl", rtype = "single",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 27089380, shortname = "Engel2016",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74596",
description = "purified populations of thymic NKT cell subsets",
protocol = "Smart-Seq2", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "U", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE63818, HiSeq2500
process_data(id = "GSE63818-GPL16791", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 26046443, shortname = "Guo2015",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63818",
description = "primordial germ cells from embryos at different times of gestation",
protocol = "Tang", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("source_name_ch1", "characteristics_ch1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = NULL, lps = "right",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE60749, HiSeq2000 (25bp reads)
process_data(id = "GSE60749-GPL13112", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 25471879, shortname = "Kumar2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60749",
description = "mESCs with various genetic perturbations, cultured in different media",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("source_name_ch1", "characteristics_ch1.1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE60749, HiSeq2500 (25bp reads)
process_data(id = "GSE60749-GPL17021", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 25471879, shortname = "Kumar2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60749",
description = "mESCs with various genetic perturbations, cultured in different media",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.k15.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("characteristics_ch1", "characteristics_ch1.1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE57872 (25bp reads)
process_data(id = "GSE57872", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 24925914, shortname = "Patel2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57872",
description = "glioblastoma cells from tumors + gliomasphere cell lines",
protocol = "SMART-Seq", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.k15.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = c("characteristics_ch1", "characteristics_ch1.1"),
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE41265
process_data(id = "GSE41265", dtype = "fl", rtype = "paired",
organism = "Mus musculus", genome = "GRCm38.84",
pmid = 23685454, shortname = "Shalek2013",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41265",
description = "stimulated immune cells",
protocol = "SMARTer", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/mus-musculus/Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Mus_musculus.GRCm38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 1, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE52529-GPL11154
process_data(id = "GSE52529-GPL11154", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 24658644, shortname = "Trapnell2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52529",
description = "primary myoblasts over a time course of serum-induced differentiation",
protocol = "SMARTer C1", protocoltype = "full-length",
dotrim = FALSE, cutadaptbin = cutadaptbin, adapterseq = NULL,
fastqcbin = fastqcbin, multiqcbin = multiqcbin,
salmonbin = salmonbin,
salmonindex = "reference-files/homo-sapiens/Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.0.6.1.sidx",
libtype = "IU", bias = FALSE,
rapmapbin = rapmapbin, rapmapindex = NULL, umis_transform = NULL, cell_barcodes = NULL,
sncol = "SampleName", groupid = "source_name_ch1",
geodata = TRUE, phenofile = NULL,
gene_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$gene_granges,
tx_granges = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.granges$tx_granges,
txgenemap = Homo_sapiens.GRCh38.84.cdna.ncrna.ercc92.txgenemap,
tmpdir = "tmp", topdir = ".",
nrw = 3, lps = "bottom",
aspects = c("fastqc", "salmon", "multiqc", "mae", "scater"),
force = FALSE)
## GSE52529-GPL16791
process_data(id = "GSE52529-GPL16791", dtype = "fl", rtype = "paired",
organism = "Homo sapiens", genome = "GRCh38.84",
pmid = 24658644, shortname = "Trapnell2014",
datalink = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52529",
description = "primary myoblasts over a time course of serum-induced differentiation",