matanhofree

crc-immune-hubs

Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organized multicellular immune hubs in human colorectal cancer"

lungTumorEvolution

Algorithms and code developed as part of the study described in Marjanovic et al.

scde

R package for analyzing single-cell RNA-seq data

bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

Bioconductor_RCy3_the_new_RCytoscape

Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST

cb_sniffer

mutation(barcode) caller for 10x single cell data

matanhofree.github.io

MatlabStan

Matlab interface to Stan, a package for Bayesian inference

mro-docker

Docker image for Microsoft R Open

salmon

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

vyaasa

Here is the demo