Pinned Repositories
amplicon_data_analysis
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
annotation
Pipeline to run multiple tools to annotate prokaryotic genomes and parse output
COEF
Collection Of Esoteric Functions
CRISPRCas_on_Plasmids
This is the code repository for reproducing analyses in the paper: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
CRISPRCasTyper
CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
DAtest
Compare different differential abundance and expression methods
DOC
Dissimilarity Overlap Curve analysis
MAGinator
MAGinator - Accurate SNV calling and profiling of MAGs
MicEco
Various functions for analysis of microbial community data
RCon3D
3D Analysis of confocal images of microbial biofilms/communities
Russel88's Repositories
Russel88/CRISPRCasTyper
CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
Russel88/DAtest
Compare different differential abundance and expression methods
Russel88/MicEco
Various functions for analysis of microbial community data
Russel88/DOC
Dissimilarity Overlap Curve analysis
Russel88/MAGinator
MAGinator - Accurate SNV calling and profiling of MAGs
Russel88/CRISPRCas_on_Plasmids
This is the code repository for reproducing analyses in the paper: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
Russel88/RCon3D
3D Analysis of confocal images of microbial biofilms/communities
Russel88/COEF
Collection Of Esoteric Functions
Russel88/annotation
Pipeline to run multiple tools to annotate prokaryotic genomes and parse output
Russel88/jobson
A platform for transforming command-line applications into a job service.
Russel88/advent_of_code
Russel88/alphafold_non_docker
AlphaFold2 non-docker setup
Russel88/bigSCale2
Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
Russel88/configs
Russel88/EsoPy
Esoteric python scripts
Russel88/growthcurver
Russel88/misc
Russel88/NGSTools
NGSTools
Russel88/run_dbcan
Run_dbcan V2, using genomes/metagenomes/proteomes of any orgaisms(prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
Russel88/Russel88.github.io
Russel88/SHEso
Bioinformatic SHell scripts of Esoteric value
Russel88/SmellyShirts
Scripts and data for: The T-shirt microbiome is distinct between individuals and shaped by washing and fabric type
Russel88/SRUFinder
Detect and subtype SRUs, mini-arrays, and CRISPR arrays by repeat matching