Pinned Repositories
AA_Comp
Evolutionary changes in aa composition of orthlogous genes during vertebrate evolution
Analyses_Pipelines
Analyses pipelines that I use for my work
ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn
applied-computational-genomics
Applied Computational Genomics Course at UU: Spring 2020
appliedgenomics2018
Materials for Spring 2018 Applied Genomics Course
bioinformatics
Course materials for Computational Biology and Bioinformatics - BI462
gene-expansion
jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
SequenceTools
Programs used in the lab for various tasks
star_protocols_wes3x
Functional code templates for the Star Protocols paper describing consolidated WES variant calling with 3 callers
UpalabdhaD's Repositories
UpalabdhaD/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
UpalabdhaD/SequenceTools
Programs used in the lab for various tasks
UpalabdhaD/ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn
UpalabdhaD/appliedgenomics2022
Materials for EN.601.449/EN.601.649 Computational Genomics: Applied Comparative Genomics
UpalabdhaD/awesome-nanopore
A curated list of awesome nanopore analysis tools.
UpalabdhaD/assembly-stats
Assembly statistic visualisation
UpalabdhaD/bioinfo_commandline_oneliners
Useful bash one-liners for bioinformatics.
UpalabdhaD/circlator
A tool to circularize genome assemblies
UpalabdhaD/compare_genomes
A comparative genomics workflow using Nextflow, conda, Julia and R
UpalabdhaD/GATK_parallel
Development of short tutorials for UNM's Center for Advanced Research Computing
UpalabdhaD/genome-assembly-workshop-2023
UpalabdhaD/GGisy
Genome-Genome circle synteny
UpalabdhaD/karyotypeR
Program for computing karyoytypes from aDNA data.
UpalabdhaD/LOST_and_FOUND
UpalabdhaD/Orthofinder_to_CAFE_scripts
This contains custom scripts to process orthofinder output for CAFE5 analysis
UpalabdhaD/Perfect-bacterial-genome-tutorial
UpalabdhaD/phylogenomics_phylogentics_tutorials
Tutorials on phylogenetic and phylogenomic inference
UpalabdhaD/pymodulon
Python package for analyzing and visualizing iModulons
UpalabdhaD/quatro-manuscript
A template for manuscripts using quatro
UpalabdhaD/Rmd-manuscript-template-dir
A template dir structure for Rmd manuscript for my taste
UpalabdhaD/score-assemblies
Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
UpalabdhaD/scRNA-seq_notes
A list of scRNA-seq analysis tools
UpalabdhaD/snakemake-training
Increasingly complete example bioinformatics workflow
UpalabdhaD/snakemake_wf_skeleton
UpalabdhaD/Test
UpalabdhaD/Tree2gd
UpalabdhaD/ud-cv
Awesome CV in R. Based on the vitae package and Dominique Makowski’s template.
UpalabdhaD/UpalabdhaD.github.io
My personal website
UpalabdhaD/UpalabdhaD_old__ghp
A beautiful, simple, clean, and responsive Jekyll theme for academics
UpalabdhaD/vcfstats
Powerful statistics for VCF files