Pinned Repositories
nf-haplocaller
Nextflow pipeline for GATK best practices (HaplotypeCaller)
SNPmatch
A simple python library to identify the most likely strain from the population
ExploringTEsinCannabisGenome
Required scripts and data for the entire analysis in Pisupati et. al. 2018
nextflow_pipelines
The set of NGS processing pipelines used at Babraham
nf-haplocaller
Nextflow pipeline for GATK best practices (HaplotypeCaller)
nf-snpmatch
Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)
pylmm
A fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.
quantitativeOmics
A toolkit for genomics, quantitative genetics
rbpisupati's Repositories
rbpisupati/quantitativeOmics
A toolkit for genomics, quantitative genetics
rbpisupati/nextflow_pipelines
The set of NGS processing pipelines used at Babraham
rbpisupati/nf-snpmatch
Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)
rbpisupati/pylmm
A fast and lightweight python-based linear mixed-model solver for use in genome-wide association studies.
rbpisupati/configs
Config files used to define parameters specific to compute environments at different Institutions
rbpisupati/cv
My CV built using RMarkdown and the pagedown package.
rbpisupati/data-repo
Repository for easy referencing NGS sequencing data
rbpisupati/downloadFromSra
Containerized NextFlow Workflow to Easily Down Sra Files
rbpisupati/freebayes
rbpisupati/GEMMA
Genome-wide Efficient Mixed Model Association
rbpisupati/limix
Linear mixed model for genomic analyses.
rbpisupati/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
rbpisupati/nf-genome_blasts
Pipeline to perform local alignments of given sequences to other genomes
rbpisupati/nf-repeatexplorer
Nextflow Pipeline for running Repeat Explorer
rbpisupati/pybstoolkit
Python API to analyse bisulfite sequencing data
rbpisupati/pyGenome
Python API for working with genome fasta/bed/annotations
rbpisupati/PyGWAS
rbpisupati/pymc-resources
PyMC educational resources
rbpisupati/pyQTL
QTL mapping using probabilistic programming (pyTorch and PyRo)
rbpisupati/R-programming-Exercises-Practice-Solution
The best way we learn anything is by practice and exercise questions. These exercises help you to improve your R programming coding skills
rbpisupati/RABBIT
A Mathematica pipeline for genetic analysis in multiparental populations
rbpisupati/rbpisupati
Config files for my GitHub profile.
rbpisupati/rethinking
Statistical Rethinking course and book package
rbpisupati/rethinking-numpyro
Statistical Rethinking (2nd ed.) with NumPyro
rbpisupati/revelio
A lightweight utility for BS-seq and MethylC-seq data which applies a double-masking procedure on bisulfite alignments, facilitating variant calling with conventional software.
rbpisupati/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
rbpisupati/sgkit
Scalable genetics toolkit
rbpisupati/statannotations
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
rbpisupati/statistical-rethinking
Following along with Statistical Rethinking text on Bayesian modeling by McElreath
rbpisupati/ViewBS
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data