Abhijit Chakraborty's repositories
LJI_RNA_SEQ_PIPELINE_V2
Snakemake based RNA-Seq QC pipeline for cloud/cluster implementation
fastbook
Draft of the fastai book
MESS
Miscellaneous Esoteric Statistical Scripts - an R package
PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
HiCtrans
HiCtrans is a pipeline to call translocations from Hi-C data
rcppexamples
Examples of using Rcpp to interface R and C++
HiC_tools
A collection of tools for Hi-C data analysis
rnafusion
RNA-seq analysis pipeline for detection gene-fusions
rnaseq
RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
r4ds
R for data science
karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
cheatsheets
RStudio Cheat Sheets
Rcpp
Seamless R and C++ Integration
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
UpSetR
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
ATACProc
ATAC-seq processing pipeline
efficientR
Efficient R programming: a book
ChIPLine
ChIP-seq analysis pipeline
HiCnv
HiCnv is used to call copy number variations and breakpoints from Hi-C data
AveSim
AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.
flowIncubator
Routines that don't belong to the core flow packages yet.
awesome-guidelines
A curated list of high quality coding style conventions and standards.
purrr
Make your pure R function purrr with functional programming