LRFreeborn

Documentation

Repository holding a wiki for Research Computing tutorials

CUmulus_tutorials

Tutorials and example workflows for CURC's on-prem cloud

Supercomputing_Spinup_Spring_2022

mantis

A package to annotate protein sequences

Filtlong

quality filtering tool for long reads

CAFE

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

cyvcf2

cython + htslib == fast VCF and BCF processing

bioicons

A library of free open source icons for science illustrations in biology and chemistry

HPC_schedulers

Which schedulers are the most popular on current HPC systems?

scanpy

Single-cell analysis in Python. Scales to >1M cells.

gosling.js

Grammar of Scalable Linked Interactive Nucleotide Graphics

sra-tools

SRA Tools

funannotate

Eukaryotic Genome Annotation Pipeline

containers

Bioinformatics containers

chromoMap

:exclamation: This is a read-only mirror of the CRAN R package repository. chromoMap — Interactive Genomic Visualization of Biological Data

de-novo-transcriptome-assembly-pipeline

Combined de novo transcriptome assembly - multiple assemblers - multiple parameters

snpToolkit

gwas-vcf-specification

Specification for the GWAS-VCF format (manuscript in preparation)

2021-GGG298

Winter 2021, GGG 298 - Tools for Data Intensive Research - UC Davis

oneliners

Useful bash one-liners for bioinformatics.

tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

shiny

Easy interactive web applications with R

Liftoff

An accurate GFF3/GTF lift over pipeline

voila

Voilà turns Jupyter notebooks into standalone web applications

bamsnap

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

drep

Rapid comparison and dereplication of genomes

NCGAS-cloud-workshop

NCGAS Cloud Workshop