matanhofree
I am a computational biologist specializing in cancer systems biology.
Broad Institute Cambridge, MA; Rehovot, Israel
Pinned Repositories
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
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.
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
scde
R package for analyzing single-cell RNA-seq data
matanhofree's Repositories
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"
matanhofree/lungTumorEvolution
Algorithms and code developed as part of the study described in Marjanovic et al.
matanhofree/scde
R package for analyzing single-cell RNA-seq data
matanhofree/bcbio-nextgen
Best-practice pipelines for fully automated high throughput sequencing analysis
matanhofree/Bioconductor_RCy3_the_new_RCytoscape
Update RCytoscape to work for Cytoscape 3.0 and higher using CyREST
matanhofree/cb_sniffer
mutation(barcode) caller for 10x single cell data
matanhofree/matanhofree.github.io
matanhofree/MatlabStan
Matlab interface to Stan, a package for Bayesian inference
matanhofree/mro-docker
Docker image for Microsoft R Open
matanhofree/salmon
Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
matanhofree/SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
matanhofree/vyaasa
Here is the demo