Owner
broadinstitute
73 indexed repositories · View on GitHub
-
gatk
Official code repository for GATK versions 4 and up
Java · 2000 stars
-
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale product...
Scala · 1082 stars
-
picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Java · 1077 stars
-
CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Python · 423 stars
-
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
Python · 269 stars
-
warp
Warp Analysis Research Pipelines
Jupyter Notebook · 230 stars
-
seqr
web-based analysis tool for rare disease genomics
Python · 219 stars
-
gatk-sv
A structural variation pipeline for short-read sequencing
Python · 208 stars
-
viral-ngs
viral-ngs: command line tools and wrappers for processing raw viral genomic data
Python · 197 stars
-
Python · 180 stars
-
long-read-pipelines
Long read production pipelines
Jupyter Notebook · 152 stars
-
cellpainting-gallery
Cell Painting Gallery
140 stars
-
Drop-seq
Java tools for analyzing Drop-seq data
Jupyter Notebook · 136 stars
-
gnomad_methods
Hail helper functions for the gnomAD project and Translational Genomics Group
Python · 102 stars
-
gnomad-browser
Explore gnomAD datasets on the web
TypeScript · 91 stars
-
viral-pipelines
viral-ngs: complete pipelines
WDL · 75 stars
-
Jupyter Notebook · 70 stars
-
pyqtl
Collection of analysis tools for quantitative trait loci
Python · 66 stars
-
celldega
Spatial and multiomic visualization and analysis library
Jupyter Notebook · 60 stars
-
delphy
Fast, scalable, accurate and accessible Bayesian phylogenetics
C++ · 50 stars
- 53 more repositories live on View on GitHub
-
Difficulty 1/5 1-3 hours Newbie friendliness 90/100
broadinstitute/gatk-sv#965 ·
-
Difficulty 4/5 3-5 days Newbie friendliness 25/100
-
Difficulty 4/5 3-5 days Newbie friendliness 38/100
broadinstitute/cromwell#7904 ·
-
broadinstitute/seqr#5592 · 1 assignee ·
-
human only ? Open
Difficulty 5/5 Over a week Newbie friendliness 25/100
broadinstitute/Himito#37 · 1 comment ·
-
Difficulty 5/5 Over a week Newbie friendliness 25/100
broadinstitute/EmmaEmb#21 ·
-
Difficulty 4/5 3-5 days Newbie friendliness 55/100
-
feature request
Difficulty 4/5 3-5 days Newbie friendliness 55/100
broadinstitute/seqr#5584 · 3 comments ·
-
feature request
Difficulty 5/5 Over a week Newbie friendliness 42/100
broadinstitute/seqr#5583 · 2 comments ·
-
Difficulty 4/5 3-5 days Newbie friendliness 35/100
-
Difficulty 4/5 3-5 days Newbie friendliness 35/100
-
Difficulty 5/5 Over a week Newbie friendliness 35/100
broadinstitute/ABC-Enhancer-Gene-Prediction#281 · 1 comment ·
-
Difficulty 5/5 Over a week Newbie friendliness 35/100
broadinstitute/exome-results-browsers#223 · 2 comments ·
-
Difficulty 4/5 3-5 days Newbie friendliness 55/100
-
broadinstitute/exome-results-browsers#221 · 1 comment · 1 assignee ·
-
broadinstitute/exome-results-browsers#220 · 1 assignee ·
-
broadinstitute/exome-results-browsers#218 · 1 assignee ·
-
Epic
Difficulty 5/5 Over a week Newbie friendliness 20/100
broadinstitute/exome-results-browsers#217 · 1 comment ·
-
good first issue
Difficulty 4/5 3-5 days Newbie friendliness 45/100
broadinstitute/gnomad-browser#1955 · 1 comment ·
-
Difficulty 1/5 Under an hour Newbie friendliness 86/100
broadinstitute/CellBender#478 ·
-
Difficulty 5/5 Over a week Newbie friendliness 30/100
broadinstitute/seqr#5570 · 1 comment · 1 reaction ·
-
Difficulty 3/5 1-2 days Newbie friendliness 55/100
broadinstitute/warp#1952 · 2 comments ·
-
Difficulty 3/5 1-2 days Newbie friendliness 58/100
broadinstitute/gnomad-browser#1943 ·
-
Standalone mode Open
Difficulty 5/5 Over a week Newbie friendliness 25/100
-
enhancement
Difficulty 4/5 3-5 days Newbie friendliness 48/100
-
Difficulty 2/5 1-3 hours Newbie friendliness 72/100
broadinstitute/cellpainting-gallery#183 · 1 comment ·
-
broadinstitute/gnomad-browser#1942 · 1 comment · 1 assignee ·
-
broadinstitute/gnomad-browser#1941 · 4 assignees ·
-
broadinstitute/gnomad-browser#1940 · 4 assignees ·
-
Plan gnomAD Parquet Open
broadinstitute/gnomad-browser#1939 · 4 assignees ·
-
bug
Difficulty 4/5 3-5 days Newbie friendliness 55/100
broadinstitute/celldega#333 · 2 comments ·
-
Triage: Dev Triage: PM
Difficulty 5/5 Over a week Newbie friendliness 25/100
broadinstitute/gnomad-browser#1938 ·
-
Triage: PM
Difficulty 3/5 1-2 days Newbie friendliness 64/100
broadinstitute/gnomad-browser#1937 ·
-
feature request
broadinstitute/seqr#5563 · 1 assignee ·
-
Difficulty 5/5 Over a week Newbie friendliness 35/100
-
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
-
Difficulty 5/5 Over a week Newbie friendliness 25/100
broadinstitute/BE3D#24 · 1 comment ·
-
enhancement priority-medium
broadinstitute/mskkp-tissue-champion-initiative#4 · 1 assignee ·
-
Funcotator mis-classifies stop-retained indels as FRAME_SHIFT_* (should be SILENT / stop-retained) Open
Difficulty 4/5 3-5 days Newbie friendliness 48/100
broadinstitute/gatk#9417 ·
-
enhancement
broadinstitute/dig-knowledge-graph#3 · 1 assignee ·
-
enhancement
broadinstitute/dig-knowledge-graph#2 · 1 assignee ·
-
Add mise Open
Difficulty 4/5 3-5 days Newbie friendliness 48/100
-
Difficulty 3/5 1-2 days Newbie friendliness 50/100
broadinstitute/celldega#332 · 2 comments · 1 reaction ·
-
Difficulty 2/5 1-3 hours Newbie friendliness 58/100
broadinstitute/gatk-sv#956 ·
-
Difficulty 3/5 1-2 days Newbie friendliness 72/100
broadinstitute/CellBender#474 ·
-
Difficulty 5/5 Over a week Newbie friendliness 10/100
broadinstitute/warp#1927 ·
-
Difficulty 5/5 Over a week Newbie friendliness 30/100
-
enhancement
Difficulty 4/5 3-5 days Newbie friendliness 52/100
broadinstitute/viral-references#38 · 3 comments ·
-
enhancement
Difficulty 2/5 1-3 hours Newbie friendliness 65/100
broadinstitute/dapper#8 · 1 comment ·
-
Difficulty 1/5 Under an hour Newbie friendliness 84/100
broadinstitute/CellBender#462 · 1 comment ·
Showing the newest 100
This page lists what was indexed most recently. Advanced filter has the whole inventory, narrowed by language, difficulty and how long a task takes.