23 Dec 2017 by sammons

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!

DEseq2

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)

Intro to Next-Gen Sequencing : A completely non-comprehensive introduction into next-gen sequencing. Primarily designed as part of a larger bootcamp held @ UAlbany

Getting Started with Next-Gen Sequencing : Tips and tricks for getting started in sequencing at UAlbany

Applications: ATAC-seq : Data I presented that turned into this paper with the Wherry lab @ the University of Pennsylvania