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awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

camoco

Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes.

caper

Cromwell/WDL wrapper for Python

cob

The gene CO-expression Browser

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

demowags

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

egglimputationpipeline

ems_gwa

equcab3nice

Some scripts to pull the canonical FASTA file from NCBI and make it nice

fastp

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

gatk-docs

Documentation archive for GATK tools and workflows

glbio-2021

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

horsestuff

immune_receptor_network-generation

Generating a data framework for B-cell and T-cell receptor sequencing data using network analysis from which biological information may be derived

imnet

imNet: a Sequence Network Construction Toolkit

indexforthefuture

Make nice and generate EC3 indices.

instructor-training

Instructor Training

library-imgt

IMGT segment library converted to RepSeq.IO JSON format

lncrna_time_course

This repository was created to assist with the reproducibility of all of the analyses presented in the published lncRNA time course manuscript.

locuspocus

Genetic coordinates so simple, it feels like MAGIC!

minus80

Freeze and integrate biological datasets.

mirec

An error correction tool for miRNA reads at single-base resolution

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

musclefattissuenetwork

Muscle Fat Tissue Network Comparison

neat

parallel-fastq-dump

parallel fastq-dump wrapper

partis

B- and T-cell receptor sequence annotation, simulation, clonal family, and germline inference