Pinned Repositories
dry-guide
parisodlab.github.io
snakeGATK4_v2
assembly-stats
Assembly statistic visualisation
ComparativeGenomics
A pipeline for processing data in a comparative genomics project.
Diabroticum-Metatranscriptome
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
snakeDeepvariant
snakemake Deepvariant
TEPID-fix
UNIX-notes
Tips and tricks for advanced UNIX user
rimjhimroy's Repositories
rimjhimroy/ComparativeGenomics
A pipeline for processing data in a comparative genomics project.
rimjhimroy/Diabroticum-Metatranscriptome
rimjhimroy/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
rimjhimroy/dry-guide
The Guide to Computing in the Andersen Lab
rimjhimroy/EMBLmyGFF3
An efficient way to convert gff3 annotation files into EMBL format ready to submit.
rimjhimroy/GWA_tutorial
A comprehensive tutorial about GWAS and PRS
rimjhimroy/ITIPs
Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data
rimjhimroy/jekyll-theme-minimal-resume
Simple Jekyll theme for a minimal resume website: https://jekyll-theme-minimal-resume.netlify.com/
rimjhimroy/snakeDeepvariant
snakemake Deepvariant
rimjhimroy/snakeGATK4
rimjhimroy/snakeTEPID
rimjhimroy/TEPID-fix
rimjhimroy/katacoda-scenarios-1
Katacoda Scenarios
rimjhimroy/katacoda_test
rimjhimroy/plastid_sequence_analysis
Analysis of plastid sequence
rimjhimroy/popgen
Population genetics analyses
rimjhimroy/popgen-notes
Population genetics notes
rimjhimroy/r-conda
R and RStudio via conda packages in repo2docker
rimjhimroy/repeat_files
rimjhimroy/residual-tetrasomy
For characterization of residually tetrasomic regions
rimjhimroy/rna-seq-pop
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
rimjhimroy/SnakeGATK
rimjhimroy/snp-calling-scripts
rimjhimroy/So2
So2 TE Bioinformatic ressources -- Parisot et al. 2020
rimjhimroy/stacks_workflow
RADseq workflow built around STACKS
rimjhimroy/SummerSchool_2023_Moeko
rimjhimroy/TE_ManAnnot
Accompanying repository for our publications on manual curation methods for Transposable Elements.
rimjhimroy/TEPID-run
rimjhimroy/TEscripts
Scripts used in Transposable element annotation
rimjhimroy/wgd
Python package and CLI for whole-genome duplication related analyses