Name: Sourya Bhattacharyya
Type: User
Company: La Jolla Institute for Immunology
Bio: Instructor, La Jolla Institute for Immunology
La Jolla, CA 92037, USA
Twitter: SouryaBhattach5
Location: United States
Blog: https://sites.google.com/site/souryacse/
Sourya Bhattacharyya's Projects
Predicting gene Expression from chromatin conformation capture (3C)
Species tree estimation using accumulated coalescence rank and excess gene leaves count
ATAC-seq processing pipeline
Scripts for bulk RNA-seq analysis
ChIP-seq analysis pipeline
Co-localization analysis between reference GWAS and eQTL summary statistics
COSPEDTree-II: Improved couplet based phylogenetic supertree
Species tree estimation using couplet supertree technique
COuplet based Phylogenetic Supertree algorithm, using Equivalence partitioning and DAG formation
Couplet Supertree construction (an improved version of COSPEDTree package)
COSPEDTree with branch length assignment, using weighted input trees
Branch Length assignment to a Custom input SuperTree topology, given a set of input weighted (with branch lengths) phylogenetic trees
Code for the book Deep Learning with PyTorch by Eli Stevens, Luca Antiga, and Thomas Viehmann.
The fastai book, published as Jupyter Notebooks
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Statistically Significant loops from HiChIP data
Species tree estimation using Internode Distance and eXcess Lineage
Interaction QTL (IQTL) using HiChIP contacts
Literature Review
Stratified LD score regression analysis
Single cell RNA-seq analysis
Deep probabilistic analysis of single-cell omics data
Config files for my GitHub profile.
Implements species tree construction from incongruent gene trees with Incomplete Lineage Sorting (ILS) using a variety of existing methods - 1) STAR 2) STEAC (Liu et. al. 2009), 3) GLASS (Roch et. al. 2010), 4) NJ-st (Liu et. al. 2011)