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aneuploidy-survival

Python scripts to support analysis of whole chromosome and arm-length aneuploidy.

ascat

ASCAT R package

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

awesome-sequencing-tech-papers

A collection of publications on comparison of high-throughput sequencing technologies.

aws-cli

Universal Command Line Interface for Amazon Web Services

bamslam

Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files

bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.

biopython

Official git repository for Biopython (originally converted from CVS)

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

brass

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

cava

CAVA (Clinical Annotation of VAriants)

compassql

CompassQL Query Language for visualization recommendation.

customprodbj

Immunopeptidome project and pipeline

deconstructsigs

deconstructSigs

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

dna2proteins

A Python script to translate DNA sequences to protein sequences

ensembl-pipeline

*DEPRECATED* Job management for the Ensembl Genebuild pipeline

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

ethseq

Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data

fragpipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

fselectorrcpp

Rcpp (free of Java/Weka) implementation of FSelector entropy-based feature selection algorithms with a sparse matrix support

g3viz

Lollipop-diagram to interactively visualize genetic mutations

gatk

Official code repository for GATK versions 4 and up

gatk4-exome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.

get-gene-info

Retrieving HGNC gene symbol reports (human genes only) via a list of gene IDs.

ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

ggsci

🦄 Scientific journal and sci-fi themed color palettes for ggplot2

hgnc-gene-family-mapper

Draws a map of a HGNC gene family hierarchy for a family

hifi-human-wgs-wdl