asafpr

RILseq

RILseq computational protocol

domain_classifier

Classify sequence to a taxonomic domain using PFAM domains

build_kraken2

Use domain classifier to build kraken2 DB

covid-model

RNA

measuring properties of RNA like conservation(actually DNA) and accessibility

biopython

Official git repository for Biopython (converted from CVS)

COVID19_data

Code stubs for data analysis regarding COVID19

bioconda-recipes

Conda recipes for the bioconda channel.

biom-format

The Biological Observation Matrix (BIOM) Format Project

CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

configs

Config files used to define parameters specific to compute environments at different Institutions

Corekaburra

Program to find core gene consensus synteny, hotspots between these, and construct spatially aware multiple sequence alignments of core genes

count_PE_fragments

Count number of paired-end RNAseq fragments mapped to each gene in bacterial genomes

cowplot

drep

Rapid comparison and dereplication of genomes

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

FusorSV

A Data Fusion Method for Multi Source (VCF4.0+) Structural Variation Analysis

GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

jax-jupyter

Jackson Labs hands-on workshop material for using Jupyter Notebooks on CloudOS

network_scripts

pro_clash

A python package and scripts to process PRO-CLASH experiments

qtl2

QTL analysis software for high-dimensional data and complex cross designs

RILseq_accessories

Accessory scripts for RILseq including generating microarray plots and MEME

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

RNAseq_scripts

Some short scripts to manipulate RNAseq libraries

rt-from-frequency-dynamics

singularity

Singularity description files

SpliceAI

A deep learning-based tool to identify splice variants

sRNA_finder

Look for short sequences in bacterial genomes