GitHub

Instructor (January 2021 - Present)

Postdoctoral researcher (April 2017 - December 2020)

La Jolla Institute for Immunology, La Jolla, CA, USA

1. FitHiChIP: method to infer statistically significant interactions from HiChIP data. Also applicable to other 3C assays like Hi-C, ChIA-PET, or promoter capture Hi-C (GitHub) (manuscript)  

2. DiffHiChIP: method to infer statistically significant differential chromatin interactions from HiChIP and other 3C assays like Hi-C, ChIA-PET, or promoter capture Hi-C (GitHub) (Manuscript)

3. pieQTL: promoter interacting eQTL - a technique to infer potentially functional eQTLs using HiChIP.        (GitHub)     (manuscript)

4. FitHiC2: inferring statistically significant interactions in Hi-C data.          (GitHub)      (manuscript)

5. IQTL: Identifying genetic variants associated with chromatin looping and genome function   (GitHub - under construction) 

6. ChIPLine: A pipeline for ChIP-seq data analysis        (GitHub)

7. ATACProc: ATAC-seq data analysis pipeline              (GitHub)

8. RNA-seq data processing scripts (GitHub)

   • Pipeline (GitHub), Differential gene analysis by DESeq2 (GitHub), Pathway analysis (GitHub), WGCNA (GitHub)

9. Single-cell RNA-seq data analysis scripts (using Seurat) (GitHub)

10. Multi-omic single-cell data analysis scripts (GitHub)

    • ArchR (GitHub)

    • Signac (GitHub)

11. FineMap: A pipeline to generate fine-mapped eQTLs. Uses the package FINEMAP (http://www.christianbenner.com/)         (GitHub)

12. Colocalization: A pipeline to identify the colocalized variants between the eQTL and GWAS summary statistics. Based on the R package coloc (https://chr1swallace.github.io/coloc/index.html).      (GitHub)

13. S_LDSC: A pipeline to implement the stratified LD score regression analysis. Used to compute the enrichment of annotations (like chromatin regions, predefined variants, or eQTLs) with respect to a given GWAS summary statistics. Based on the Stratified LD score regression package (https://github.com/bulik/ldsc).     (GitHub)

14. Various utility scripts for chromatin conformation capture (3C) data analysis - used in the above mentioned projects (GitHub)

Ph.D. research (July 2012 - August 2017)

Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, India

• COSPEDTree-II: An extension of COSPEDTree, in terms of improved running time, and resolving the topological conflicts among a group of closely related species.      (manuscript)    (GitHub)

• IDXL:  Another method to infer the species trees from incongruent gene trees due to ILS or DC. Proposes two metrics, namely Internode Distance and Excess Gene Leaf Count, for species tree inference. Performs better than AcRNJ and COSPEDSpec.    (manuscript)    (GitHub) 

• AcRNJ: Another method to infer the species trees from incongruent gene trees due to ILS or DC. Proposes two metrics, namely Accumulated Coalescence Rank and Excess Gene Count, to infer the species trees.       (manuscript)    (GitHub)

• COSPEDSpec: Infers species trees (ideal or most probable evolutionary relationship among a group of species or taxa) from the gene trees (evolutionary relationship among a group of taxa, with respect to a specific gene; also called gene lineages), where the gene trees exhibit incongruent (discordant) topologies due to incomplete lineage sorting (ILS) or Deep Coalescence (DC).      (manuscript)      (GitHub)

• CospedTreeBL: An extension of COSPEDTree, where the evolutionary tree branches (edges) also have weights (representing the evolutionary distance among a group of taxa). The tool creates a weighted supertree from the input gene trees.  (GitHub)

• COSPEDTree: COuplet Supertree by Equivalence Partitioning of taxa set and DAG formation. Given a set of phylogenetic trees (evolutionary relationships) with conflicting tree topologies, the tool creates a phylogenetic supertree consisting of all the taxa and their consensus relationship.   (manuscript_TCBB)     (manuscript_ACM_BCB)    (GitHub)