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    73 repositories

    • trichelab.github.io

      Public
      Organization site on github.io (supposedly)
      JavaScript
      •8•0•1•1•Updated Nov 14, 2024Nov 14, 2024

    • singlet

      Public
      Single-cell analysis with non-negative matrix factorization
      C++
      •13•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • methBlockR

      Public
      What the Package Does (One Line, Title Case)
      R
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • FileSetExperiment

      Public
      A rectangular FileSet-backed object with rowData and colData
      R
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • bamSliceR

      Public
      Slice and dice controlled-access BAMs for thousands of samples
      R
      •2•1•2•0•Updated Oct 8, 2024Oct 8, 2024

    • conumee2

      Public
      spare copy of conumee2 in case it goes missing
      R
      •
      MIT License
      •6•0•0•0•Updated Jul 26, 2024Jul 26, 2024

    • nanoranger

      Public
      simplified cellranger for long-read data
      Python
      •
      MIT License
      •5•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • STAAR

      Public
      An R package for performing STAAR procedure in whole-genome sequencing studies
      C++
      •
      GNU General Public License v3.0
      •42•0•0•0•Updated May 21, 2024May 21, 2024

    • biscuiteer

      Public
      tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output
      R
      •11•5•5•1•Updated Mar 1, 2024Mar 1, 2024

    • GMMAT

      Public
      Generalized linear Mixed Model Association Tests
      C
      •
      Other
      •22•0•0•0•Updated Nov 17, 2023Nov 17, 2023

    • plotfly

      Public
      plotly automation for various dimension reduction swappage
      R
      •
      Other
      •1•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • sturgeon

      Public
      Python
      •
      Other
      •8•0•0•0•Updated Oct 27, 2023Oct 27, 2023

    • cropcircle

      Public
      metabolomics imputation, factorization, manipulation
      R
      •
      Other
      •1•1•0•0•Updated Oct 19, 2023Oct 19, 2023

    • scGate

      Public
      marker-based purification of cell types from single-cell RNA-seq datasets
      R
      •12•0•0•0•Updated Oct 18, 2023Oct 18, 2023

    • Schiele

      Public
      Like Seurat, but for people with less than 1024GB of RAM
      R
      •
      Other
      •0•0•1•0•Updated Oct 4, 2023Oct 4, 2023

    • biscuiteerData

      Public
      R
      •1•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • chromophobe

      Public
      a package to handle ChromHMM (http://compbio.mit.edu/ChromHMM/) and similar segmentation models in R
      R
      •3•0•0•0•Updated Jun 15, 2023Jun 15, 2023

    • Fig2

      Public
      Rmarkdown output
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 23, 2023May 23, 2023

    • cell-census

      Public
      CELLxGENE Cell Census
      Jupyter Notebook
      •
      MIT License
      •22•0•0•0•Updated Jan 12, 2023Jan 12, 2023

    • pluto-sdk-R

      Public
      R package for interacting with the Pluto API
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Dec 16, 2022Dec 16, 2022

    • RcppML

      Public
      Rcpp Machine Learning: Fast robust NMF, divisive clustering, and more
      C++
      •
      GNU General Public License v2.0
      •16•0•0•0•Updated Nov 3, 2022Nov 3, 2022

    • GEMLI

      Public
      GEMLI fork
      R
      •5•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • spiky

      Public
      R
      •5•2•8•0•Updated Sep 16, 2022Sep 16, 2022

    • scing

      Public
      SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)
      Python
      •
      MIT License
      •3•0•0•0•Updated Jun 15, 2022Jun 15, 2022

    • UMIcountR

      Public
      R
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated May 23, 2022May 23, 2022

    • velocessor

      Public
      velocity processor
      R
      •
      Other
      •2•2•0•0•Updated Jan 4, 2022Jan 4, 2022

    • WorldsSimplestCodeReview

      Public
      The importance of replication and the unimpeachable virtues of self-correcting science
      R
      •
      Creative Commons Zero v1.0 Universal
      •16•0•0•0•Updated Dec 3, 2021Dec 3, 2021

    • ExpDesign2021

      Public
      A package to ensure that all dependencies are installed for Experimental Design & Biostats practical sessions. Scroll down to the README for installation details.
      R
      •
      Other
      •16•0•0•0•Updated Nov 8, 2021Nov 8, 2021

    • compartmap

      Public
      Chromatin compartment inference from ATACseq, RNAseq, and DNA methylation
      R
      •
      Other
      •9•1•0•0•Updated Jun 25, 2021Jun 25, 2021

    • MTseeker

      Public
      mitochondrial variant analysis tools
      rgeneticsbioconductormitochondria
      R
      •9•13•4•0•Updated Mar 4, 2021Mar 4, 2021