Bioinformatics

1) Genomic data visualization and analysis basics (in python) (link)

2) R package biomaRt to query Ensembl dataset (link, biomaRt user guide)

3) BioStrings package to read and write fasta files in R (link)

4) A great collection of Unix commands for bioinformatics (pdf)

5) Great resources on bioinformatics and tutorials (link)

6) Programming tools: R, Python, UNIX shell scripts and other data science tools

7) BLASTP for protein blast and peptidematch

Online database for querying peptides

8) biopython package for Python

9) Shell script and python script to parse output from SignalP bioinformatics software (on bitbucket)

10) Shell script and python script to parse output from PSortB bioinformatics package (on bitbucket)

11) samtools for analyzing bam files (tutorial and exercises)

12) bedtools

13) Transcriptomics tools: tophat (align reads), cufflinks (assemble)

14) Great tutorial on RNA-Seq and NGS data analysis (from HSPH) and other bioinformatics training material (HSPH)

15) Single-cell techniques tutorial (link)

16) Open source tools from Broad Institute (MORPHEUS)

17) Using limma to analyze microarray data (tutorial)

18) Cytoscape and plugins for network visualization (link)

19) Find new targets for validation (link)

20) Publicly available genomic data on NIH GEO (link)

21) Book by Rafael Irizarry on Data Analysis for Life Sciences (link)

22) Cell type enrichment inference from microarray data (CTen) and cell type deconvolution (CellMix)

23) R code for converting from Entrez ID to Ensembl ID using annotation packages (on bitbucket)

24) Geneset over-enrichment analysis using Fisher test (link)

25) Visualizing GO (Gene Ontology) term over-enrichment (link) (link) (topGO R package)

26) R package for exploring single-cell sequencing data (link)

27) Other code snippets and vignettes for bioinformatics see my own software page (link)

28) Repository of single-cell datasets (link)

Repository of single-cell analysis tools (link)

29) Protein Atlas (link) (link) (proteomicsdb)

30) Immune Epitope Database (IEDB) (link)

Epitope dataset download (link)

Script or REST API to query IEDB (link)

curl --data "method=recommended&sequence_text=%3Epeptide1%0AGHAHKVPRRLLKAAR%0A%3Epeptide2%0ALKAADASADADGSGSGSGSG&allele=HLA-DRB1*01:01,HLA-DRB1*03:01" http://tools-cluster-interface.iedb.org/tools_api/mhcii/ > out_curl.txt'

31) Single-cell receptor ligand communication network software (link)

32) Find your genes in other single-cell datasets and mouse ATLAS (link)

33) 3D structural data and visualization for ligands (NGLViewer)

33) Read structural information on ligands and proteins from PDB (Protein Data Bank) (link)

Use python to read in these files (link) or BioPython

35) WGCNA (link)

36) Galaxy tool for open source bioinformatics (link)

37) Sequence analysis using GATK (link)

38) Dealing with GWAS and eQTL data (link)