R packages by syedhaider5

chicane - Capture Hi-C Analysis Engine

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.

Last updated 3 years ago

2.75 score 28 scripts 440 downloads

SIMMS - Subnetwork Integration for Multi-Modal Signatures

Algorithms to create prognostic biomarkers using biological genesets or networks.

Last updated 3 years ago

2.30 score 20 scripts 367 downloads

iDOS - Integrated Discovery of Oncogenic Signatures

A method to integrate molecular profiles of cancer patients (gene copy number and mRNA abundance) to identify candidate gain of function alterations. These candidate alterations can be subsequently further tested to discover cancer driver alterations. Briefly, this method tests of genomic correlates of mRNA dysregulation and prioritise those where DNA gains/amplifications are associated with elevated mRNA expression of the same gene. For details see, Haider S et al. (2016) "Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia", Genome Biology, <https://pubmed.ncbi.nlm.nih.gov/27358048/>.

Last updated 1 years ago

1.00 score 10 scripts 174 downloads