Links I really like
- UCSC Genome Browser
- Ubiquitous and fantastically data rich, UCSC Genome Browser is my go-to.
- WashU Epigenome Browswer
- Excellent 3D visualization tools as well as host to a number of consortium data hubs
- Cancer Cell Line Encyclopedia
- Search for your favorite genes and compare expression across multiple cancer cell lines. Very well done.
- HOMER
- One of the best annotated software suites, this is still my favorite semi-integrated next-gen sequencing analysis software. Bonus for being great at its original function: DNA motif analysis
- Bedtools
- Indispensable tool for analysis of genomic intervals/peak locations.
- Homebrew
- Easiest way to install and update command line software tools on Mac.
- Homebrew Formulas
- Nice list of software that can be installed/managed by homebrew.
- Gene Expression Omnibus
- NIH-funded repository for genomics data of all types
- Sequence Read Archive
- NIH-funded repository for next-generation sequencing reads.
- deeptools
- Very nice suite of tools for some ChIP-seq/RNA-seq applications; many uses!
- STAR Aligner
- Super fast and accurate aligner: requires high RAM for mammalian genomes, but speed can’t be beat.
- Bowtie2
- My favorite short read aligner (mainly because I know how to use it).
- HOCOMOCO
- Nice database of DNA-binding protein motifs
- Firebrowse
- Integration of (primarily) the Cancer Genome Atlas (TCGA) data
- cBioPortal
- Integration of TCGA and many other datasets
- EMBOSS
- Software suite that performs numerous DNA/RNA sequence manipulations
- JASPAR
- Transcription factor binding motif database
- Software Carpentry
- Learn how to code (I need to do this)