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Jessica Blanton edited this page Jul 26, 2016
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- de novo RNA: Transcriptomic analysis
- de novo DNA
- mapping to references
- tools
- bow tie
- BWA
- CLC (paid reco)
- RAD-Seq (stacks)
- Snp analyses/variant calling
- Structure
- Statistical analysis with
- The CIPRES Science Gateway V. 3.3 - free, online interface for highly used software!
- Alignment software MUSCLE MAAFT etc
- Visualization FigTree (desktop download), iTOL (online with export)
- Phylogenomics
- BLAST+ algorithm
- Diamond algorithm: Using Diamond for BLAST-like searches
- NCBI and custom BLAST databases
- Taxonomic assignment Databases
- Eukaryotic SILVA and PR2
- Amplicon sequencing and analysis
- Presentations from QIIME workshop June 29, 2016 QIIME_Workflow, Analysis_Principles, Advanced_Analysis
- Shotgun metagenomic analysis
- Darkhorse
- Visualization for metagenomes Anvi'o
- Metabolic reconstruction
- Natural products
- Variants
- Using Mothur and Qiime- solutions to common problems
- ANI
- IMG/JGI
- Galaxy
- DESeq2: differential expression
- Tuxedo suite
Tools: miscellaneous recommendations
Markdown cheatsheets
Digital notebooks - jupyter (ipython)
- Introduction and online playground
- Running a remote notebook
- Using multiple languages (kernals)
[Languages: coding basics](Coding Basics)
- bash
- python
- perl
- R
- SQL
General computing
- Shell essentials: The Shell, by ctb
- Version control with git / github
- File manipulation in bash
- File manipulation in R
Data management
Bioinformatics wrapper pkgs
- BioJava
- Biopython
- Bioconductor
Data Quality check, trimming, filtering
Clustering methods and visualization
- Network analyses
- k-means analysis
Visualization methods
- Inkscape
- UCSD Triton cluster
- Extreme Science and Engineering Discovery Environment - XSEDE
- Amazon Web Services - AWS
- Meeting Schedule and Speakers
- UCSD Bioinformatics courses
- Workshops
-
The BUG project
- Meetup schedule
- How to write tutorials
- How to write topic wikipages
- Logo competition!
- Markdown documents
- Digital notebooks - jupyter (ipython)
- Languages: coding basics
- General computing
- Data management
- Bioinformatics wrapper pkgs
- Data Quality check, trimming, filtering
- Clustering methods and visualization
- Visualization methods