Pinned Repositories
GTA_Hunter
Classification of GTA Genes using Machine Learning
MetaComp
Toolkit for comparative metagenomics in EDGE
metamer
Cluster shotgun sequencing samples
PhaME
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
PhaME-old
piret
Pythonic PiReT
Tools-VariantDiscovery
A list of awesome tools for discovering variants.
mshakya's Repositories
mshakya/Tools-VariantDiscovery
A list of awesome tools for discovering variants.
mshakya/metamer
Cluster shotgun sequencing samples
mshakya/GTA_Hunter
Classification of GTA Genes using Machine Learning
mshakya/PhaME
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
mshakya/PhaME-old
mshakya/piret
Pythonic PiReT
mshakya/Bacillus_Phame
mshakya/bio-jclub
Journal club website
mshakya/bioconda-recipes
Conda recipes for the bioconda channel.
mshakya/datasets-sars-cov-2
mshakya/dotfiles
:wrench: .files, including ~/.macos — sensible hacker defaults for macOS
mshakya/eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
mshakya/Hynes_Shakya_etal_MBE2016
mshakya/migun
mshakya/mshakya.github.io
mshakya/my_scripts
Collection of scripts that I use constantly.
mshakya/ncov
Nextstrain build for novel coronavirus SARS-CoV-2
mshakya/PhaME-manuscript-data
mshakya/phame_examples
Example datasets for running different instances of phame
mshakya/Phamer
mshakya/PiReT-OME
mshakya/resume
mshakya/rpiret
R functions for PiReT
mshakya/SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
mshakya/sars-cov-2_sra_mdata
mshakya/syndata
mshakya/Tools-Assemblers
mshakya/Tools-Binning
List of Tools that bins contigs and reads.
mshakya/Tools-TreeCompare
List of tools that compare phylogenies
mshakya/WorkflowPlanning
This is primarily a repo for capturing policies and discussions around the different workflows for NMDC. This is also used for project management related pieces.