pathwayanddataanalysis Goto Github PK

cancer-network

For generating a network that shows the relations of the observed gene alterations in a cancer patient to the known cancer genes or other custom gene sets.

causal-priors-extractor

This project extracts causal priors from Pathway Commons database to use in CausalPath.

causality

Automatically exported from code.google.com/p/causality

causalpath

A project for exploring differentially active signaling paths related to proteomics datasets

causalpath-newt-webserver

causalpath-webserver

Web Server for CausalPath

cptac-gbm-survival-signature

In this analysis, we check if the survival transcriptomic signature in TCGA GBM cohort is also visible in the CPTAC GBM cohort.

cytoscape.js

Graph theory (a.k.a. network) library for analysis and visualisation (compatible with CommonJS/Node.js/Browserify/Webpack, AMD/Require.js, npm, Bower, jspm, Meteor/Atmosphere, jQuery, and plain JS/JavaScript)

finkle-phys-479

firehose-parser

A parser for Broad Firehose

frext-to-biopax

Convertor from REACH frext format to BioPAX

gsplot

Gene set viewer

misc

Collection of several basic code

misc-helpers

Several miscellaneous python code for data processing and analysis.

misc2

misc is dead! long live the misc2

modulators

For discovering and classifying modulators of gene expression

mutation-patterns

For detecting potentially cancer-driver mutations based on their distribution compared to other genomic profiles.

mutex

Automatically exported from code.google.com/p/mutex

mutex-de-novo

Mutual exclusivity analysis developed for de novo mutations in autism datasets.

protein-site-motif

This project aims to identify motifs in protein phosphorylation sites.

repo

Repository for maven jars and other resources.

resource

Collection of code for accessing several data resources.

rnatoprotein

A linear regression framework for predicting proteomic values from transcriptomic data.

sif-explorer

A web service for graph theoretic exploration of SIF networks.

single-cell-pathway-analysis

A webserver for pathway analysis of single cell trajectories

single-cell-pathway-analysis-client

tf-activity

For inferring differential transcription factor activity using RNA expression data and transcriptional network.

tf-analysis

utility

Contains code that is often shared by many projects.