Rahul Pisupati's Projects
git repo for stats tutorials
compare a vcf to database snps
Config files used to define parameters specific to compute environments at different Institutions
My CV built using RMarkdown and the pagedown package.
Repository for easy referencing NGS sequencing data
Containerized NextFlow Workflow to Easily Down Sra Files
Required scripts and data for the entire analysis in Pisupati et. al. 2018
Genome-wide Efficient Mixed Model Association
Linear mixed model for genomic analyses.
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Mixed Model Package For Genome-wide association mapping.
The set of NGS processing pipelines used at Babraham
Pipeline to perform local alignments of given sequences to other genomes
Nextflow pipeline for GATK best practices (HaplotypeCaller)
Nextflow Pipeline for running Repeat Explorer
Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)
bsseq toolkit in python
Python API to analyse bisulfite sequencing data
Python API for working with genome fasta/bed/annotations
A fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.
PyMC educational resources
QTL mapping using probabilistic programming (pyTorch and PyRo)
Tools for making plots of genomic datasets in a genome-browser-like format
A toolkit for genomics, quantitative genetics
Learn R in simple and easy steps starting from basic to advanced concepts with examples. If you are trying to understand the R programming language as a beginner, this tutorial will give you enough understanding on almost all the concepts of the language from where you can take yourself to higher levels of expertise.
The best way we learn anything is by practice and exercise questions. These exercises help you to improve your R programming coding skills
A Mathematica pipeline for genetic analysis in multiparental populations
Config files for my GitHub profile.