matt-sd-watson

ACTINN

allennlp-reading-comprehension

annotate_ncov_trees

A workflow to automate the annotation of newick trees for COVID-19

augur

Pipeline components for real-time phylodynamic analysis

auspice

Web app for visualizing pathogen evolution

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

bioinformatics_workflows

bioinformatics workflows covering standard NGS transcriptomic analyses

civet3

CopyscAT

Inferring CNV data from single cell ATAC seq

covid-19-analysis

data visualization & widgets of covid-19 public dataset analysis using Jupyter (R & Python)

DS_jupyter

A variety of jupyter notebook exercises for data science and bioinformatics

faSomeRecords

Extracts FASTA records from multiFASTA file based on a list of FASTA headers

ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

mitch

An R package for multi-dimensional pathway enrichment analysis

MSDSHub

Hosts the website for MSDSHub.com

ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

ncov-utils

Utility scripts and modules for processing ncov19 samples using the ivar pipeline

networkD3

D3 JavaScript Network Graphs from R

nextflow_misc

Miscellaneous of development pipelines for bioinformatics processes

ogp-notes

pymongo-vcf

Integration of a MongoDB database for storing and filtering variant caller (VCF) file information

python_parsers

Python scripts for data file parsing and bulk shell script analyses for downstream data processing tools

scMatch

scMatch: a single-cell gene expression profile annotation tool using reference datasets

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

shiny.rstudio.com-tutorial

Slides and exercises for the video tutorial at https://shiny.rstudio.com/tutorial/

snipit

snipit: summarise snps relative to your reference sequence

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

TS_parse

Python scripts dedicated to automated parsing of Agilent TapeStation 2200 QC run reports for input into a LIMS system

umiread

Lightweight library for parsing quality control information for the UMIs in 10x single cell gene expression assays

vsn-pipelines

A repository of pipelines for single-cell data in Nextflow DSL2