cbg-ethz/V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Language: Jupyter Notebook - Size: 13.6 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 125 - Forks: 39

sscansan/genomics_and_GWAS_tutorials

Analysis of SNP variants, derived from chip array genotyping and HTS sequencing

Language: HTML - Size: 25.4 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 1 - Forks: 0

PoisonAlien/maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Language: R - Size: 70.1 MB - Last synced: about 2 hours ago - Pushed: 27 days ago - Stars: 415 - Forks: 215

neurogenomics/MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

Language: R - Size: 8.7 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 64 - Forks: 14

TobyBaril/EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline

Language: Python - Size: 5.03 MB - Last synced: about 3 hours ago - Pushed: about 4 hours ago - Stars: 112 - Forks: 17

cogent3/cogent3

Comparative Genomics Toolkit 3

Language: Python - Size: 41.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 93 - Forks: 52

AustralianBioCommons/human-omics-data-sharing-field-guide

Prototype for Human Genomics Data Sharing Field Guide Website

Language: TeX - Size: 3.85 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 2

broadinstitute/gatk

Official code repository for GATK versions 4 and up

Language: Java - Size: 452 MB - Last synced: about 2 hours ago - Pushed: about 5 hours ago - Stars: 1,604 - Forks: 574

bio-cr/hts.cr

HTSlib bindings for Crystal

Language: Crystal - Size: 1.79 MB - Last synced: 11 days ago - Pushed: 3 months ago - Stars: 10 - Forks: 1

GenSpectrum/cov-spectrum-website

A web platform to detect and analyze variants of SARS-CoV-2

Language: TypeScript - Size: 24.6 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 57 - Forks: 13

Database-Genius/Database-Genius.github.io

:arrow_right: Preston Hunter: world-class database designer and programmer.

Language: HTML - Size: 5.5 MB - Last synced: about 8 hours ago - Pushed: over 6 years ago - Stars: 3 - Forks: 2

bioinfodlsu/phage-host-prediction

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. Our approach improves performance and eliminates the need for manual feature engineering of phage sequences

Language: Jupyter Notebook - Size: 10.8 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 7 - Forks: 2

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 114 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 26 - Forks: 8

a-r-j/TB-Resources

List of online databases and resources for Mycobacterium Tuberculosis

Size: 10.7 KB - Last synced: about 8 hours ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1

neuhausi/canvasxpress-js

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Language: CSS - Size: 25.3 MB - Last synced: about 3 hours ago - Pushed: about 9 hours ago - Stars: 8 - Forks: 1

neuhausi/canvasXpress

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Language: R - Size: 102 MB - Last synced: about 3 hours ago - Pushed: about 9 hours ago - Stars: 286 - Forks: 42

overture-stack/website

:construction: Overture.bio website, based on Gatsby static site generator

Language: JavaScript - Size: 41.4 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1 - Forks: 2

huangnengCSU/longcallR

LongcallR is a small variant caller for single molecule long-read RNA-seq data

Language: Rust - Size: 19 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 32 - Forks: 1

BV-BRC/BV-BRC-Web

The BV-BRC Web Application

Language: JavaScript - Size: 546 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 7 - Forks: 21

andersen-lab/HCoV-19-Genomics

SARS-CoV-2 genomics

Size: 166 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 13 - Forks: 4

GMOD/jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

Language: TypeScript - Size: 191 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 186 - Forks: 58

PavlidisLab/Gemma

Genomics data re-analysis

Language: Java - Size: 459 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 18 - Forks: 6

brentp/variantkey-nim

nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64

Language: C - Size: 21.5 KB - Last synced: about 12 hours ago - Pushed: over 5 years ago - Stars: 4 - Forks: 0

brentp/pedfile

pedigree file parsing and relatedness calculations for nim

Language: Nim - Size: 39.1 KB - Last synced: about 12 hours ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

brentp/indelope

find large indels (in the blind spot between GATK/freebayes and SV callers)

Language: Nim - Size: 133 KB - Last synced: about 12 hours ago - Pushed: over 6 years ago - Stars: 39 - Forks: 1

brentp/hts-python

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Language: Python - Size: 606 KB - Last synced: about 12 hours ago - Pushed: about 7 years ago - Stars: 49 - Forks: 18

brentp/genoiser

use the noise

Language: Nim - Size: 1.94 MB - Last synced: about 12 hours ago - Pushed: about 4 years ago - Stars: 15 - Forks: 0

brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

Language: Cython - Size: 14.7 MB - Last synced: about 12 hours ago - Pushed: 2 months ago - Stars: 357 - Forks: 71

TheJacksonLaboratory/geneweaver-api

A system for the integration and analysis of heterogeneous functional genomics data.

Language: Python - Size: 475 KB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 0

chanzuckerberg/czid-web

Infectious Disease Sequencing Platform

Language: TypeScript - Size: 264 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 77 - Forks: 22

waldronlab/MultiAssayExperiment

Bioconductor package for management of multi-assay data

Language: R - Size: 6.85 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 69 - Forks: 32

sanger-tol/genomenote

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

Language: Groovy - Size: 3.58 MB - Last synced: 28 minutes ago - Pushed: about 14 hours ago - Stars: 19 - Forks: 3

waldronlab/VisiumIO

Import spaceranger output and 10X spatial data

Language: R - Size: 34.2 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

cmzmasek/forester

forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research

Language: Java - Size: 126 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 33 - Forks: 15

cidgoh/GRDI_AMR_One_Health

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.

Size: 158 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 6 - Forks: 0

Gagniuc/Simple-JS-implementation-of-Objective-Digital-Stains

Simple JS implementation of Objective Digital Stain (ODS) produces ODS images from DNA sequences. On ODSs, the information content (IC) is represented vertically on the y-axis and the frequency of different letters is represented horizontally on the x-axis.

Language: HTML - Size: 125 KB - Last synced: about 15 hours ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

Gagniuc/Presentations

This section contains all the original presentations from the supplementary materials related to the book entitled: Algorithms in Bioinformatics: Theory and Implementation. The presentations contain original content related to biology, bioinformatics, genetics, genomics, physics, as well as algorithms or software programming implementations.

Size: 93.3 MB - Last synced: about 15 hours ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

Gagniuc/Objective-Digital-Stains

This is an application that shows the informational structure of DNA sequences. The objective digital stain (ODS) is represented by a distribution of points on a two-dimensional image, which reflects the information structure inside a DNA/RNA sequence.

Language: HTML - Size: 111 KB - Last synced: about 15 hours ago - Pushed: about 2 years ago - Stars: 3 - Forks: 2

Gagniuc/Genomin

Genomin is an implementation for large-scale genomic analysis. It is made in Visual Basic 6.0 (VB6). It uses the seek method to generate buffers from large FASTA files (over 8 Gb).

Language: Visual Basic 6.0 - Size: 4.17 MB - Last synced: about 15 hours ago - Pushed: over 1 year ago - Stars: 3 - Forks: 3

vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Language: C++ - Size: 32.9 MB - Last synced: about 15 hours ago - Pushed: 4 days ago - Stars: 596 - Forks: 218

noamteyssier/gia

gia: Genomic Interval Arithmetic

Language: Rust - Size: 3.13 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 45 - Forks: 2

broadinstitute/gatk-sv

A structural variation pipeline for short-read sequencing

Language: Python - Size: 66.8 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 157 - Forks: 70

EUCANCan/prepy-wrapper

Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis.

Language: Python - Size: 25.4 KB - Last synced: about 19 hours ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

greenelab/deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

Language: HTML - Size: 90.9 MB - Last synced: about 5 hours ago - Pushed: over 1 year ago - Stars: 1,232 - Forks: 271

omnaest/UniProt4J

Utils for the REST API of http://www.uniprot.org

Language: Java - Size: 75.2 KB - Last synced: about 19 hours ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

omnaest/Ensembl4J

REST and FTP java utility library for the ENSEMBL API at http://rest.ensembl.org/ and http://www.ensembl.org/info/data/ftp/index.html

Language: Java - Size: 154 KB - Last synced: about 19 hours ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

broadinstitute/gnomad-browser

Explore gnomAD datasets on the web

Language: TypeScript - Size: 39.7 MB - Last synced: about 1 hour ago - Pushed: about 9 hours ago - Stars: 78 - Forks: 40

dmnfarrell/pathogenie

Desktop tool for microbial genome annotation and gene detection

Language: Jupyter Notebook - Size: 30.3 MB - Last synced: about 20 hours ago - Pushed: almost 3 years ago - Stars: 12 - Forks: 4

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 67.5 MB - Last synced: about 4 hours ago - Pushed: about 22 hours ago - Stars: 4,171 - Forks: 1,713

fpusan/SuperPang

Non-redundant pangenome assemblies from multiple genomes or bins

Language: Python - Size: 3.7 MB - Last synced: about 4 hours ago - Pushed: about 23 hours ago - Stars: 13 - Forks: 2

Nazeeefa/awesome-sequencing-tech-papers

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

Size: 163 KB - Last synced: about 4 hours ago - Pushed: 1 day ago - Stars: 26 - Forks: 3

wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

Language: JavaScript - Size: 78.7 MB - Last synced: about 4 hours ago - Pushed: 1 day ago - Stars: 265 - Forks: 113

Pathogen-Genomics-Cymru/lodestone

Mycobacterial pipeline

Language: Python - Size: 570 MB - Last synced: about 4 hours ago - Pushed: about 21 hours ago - Stars: 12 - Forks: 3

pyranges/pyranges

Performant Pythonic GenomicRanges

Language: Python - Size: 7.62 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 389 - Forks: 42

brentp/smoove

structural variant calling and genotyping with existing tools, but, smoothly.

Language: Go - Size: 2.48 MB - Last synced: about 12 hours ago - Pushed: 9 months ago - Stars: 220 - Forks: 21

bigomics/omicsplayground

Visual self-service analytics platform for big omics data.

Language: R - Size: 1.15 GB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 114 - Forks: 35

jguhlin/ODG

ODG: Omics Database Generator - Integration toolkit for -omics data

Language: Clojure - Size: 165 MB - Last synced: 1 day ago - Pushed: over 5 years ago - Stars: 7 - Forks: 4

PavlidisLab/gemma.R

An R wrapper for the Gemma RESTful API

Language: R - Size: 78.7 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 8 - Forks: 1

heche-psb/wgd Fork of arzwa/wgd

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Language: Python - Size: 182 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 14 - Forks: 0

chrovis/gnife

Gnife is a CLI tool for manipulating genomic files and data.

Language: Clojure - Size: 41 KB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

tanghaibao/jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

Language: Python - Size: 9.35 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 692 - Forks: 179

KwatMDPhD/Nucleus.jl

The nuclear package for various bioinformatics projects like GSEA.jl 🧬

Language: Julia - Size: 227 MB - Last synced: about 17 hours ago - Pushed: 1 day ago - Stars: 11 - Forks: 0

mt1022/gppy

[G]enomic [P]ositioning with [Py]thon

Language: Python - Size: 2.98 MB - Last synced: 1 day ago - Pushed: about 1 month ago - Stars: 7 - Forks: 1

oist/plessy_pairwiseGenomeComparison

Draft workflow for pairwise genome comparison

Language: Nextflow - Size: 831 KB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 4 - Forks: 2

cidgoh/nf-ncov-voc

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

Language: Python - Size: 15.2 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 4 - Forks: 4

KarchinLab/open-cravat

A modular annotation tool for genomic variants

Language: JavaScript - Size: 8.74 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 106 - Forks: 26

stjudecloud/workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Language: WDL - Size: 9.58 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 30 - Forks: 9

zyxue/zyxue.github.io

My technical blog

Language: SCSS - Size: 5.34 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

google/deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language: Python - Size: 503 MB - Last synced: about 22 hours ago - Pushed: about 1 month ago - Stars: 3,079 - Forks: 695

thierrygosselin/radiator

RADseq Data Exploration, Manipulation and Visualization using R

Language: HTML - Size: 9.67 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 57 - Forks: 22

ScienceComputing/NGSOmics_Programming

Computational biology/bioinformatics workflows, codes, and concept notes on NGS data

Language: HTML - Size: 8.13 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 5 - Forks: 0

abbvie-external/OmicNavigator

Open-Source Software for Omic Data Analysis and Visualization

Language: R - Size: 56.6 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 27 - Forks: 8

enormandeau/barque

Environmental DNA metabarcoding taxonomic identification

Language: Python - Size: 3.23 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 26 - Forks: 5

TheJacksonLaboratory/geneweaver-db

The GeneWeaver database interaction code.

Language: Python - Size: 357 KB - Last synced: 30 minutes ago - Pushed: 1 day ago - Stars: 2 - Forks: 0

zjwinn/TASSEL-VCF-Fixer

A program for fixing TASSEL produced GBS VCFs so that they are coded reference-alternate

Language: Shell - Size: 13.7 KB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

arvados/arvados

An open source platform for managing and analyzing biomedical big data

Language: Go - Size: 71.9 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 363 - Forks: 111

rwk-unil/sapphire

Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)

Language: C++ - Size: 7.17 MB - Last synced: 16 minutes ago - Pushed: 2 days ago - Stars: 8 - Forks: 1

fulcrumgenomics/fgbio

Tools for working with genomic and high throughput sequencing data.

Language: Scala - Size: 9.09 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 304 - Forks: 68

pguenzi-tiberi/Alien_index_report_generator

Language: Python - Size: 32.2 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

broadinstitute/gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group

Language: Python - Size: 5.94 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 81 - Forks: 26

fulcrumgenomics/fgpyo

Quality of life improvements for Bioinformatics in Python.

Language: Python - Size: 384 KB - Last synced: about 23 hours ago - Pushed: 14 days ago - Stars: 23 - Forks: 3

bioinf-mcb/Metagenomic-DeepFRI

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Language: Python - Size: 6.51 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 27 - Forks: 6

GCBL-NIAB/Fasta2Lineage

To assign lineage of FASTA sequences.

Language: Perl - Size: 455 KB - Last synced: about 3 hours ago - Pushed: 2 days ago - Stars: 2 - Forks: 0

Kuanhao-Chao/Kuanhao-Chao.github.io Fork of academicpages/academicpages.github.io

Kuan-Hao Chao's Website

Language: HTML - Size: 280 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 1

LooseLab/readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Language: Python - Size: 4.47 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 159 - Forks: 29

tskit-dev/tskit

Population-scale genomics

Language: Python - Size: 17.4 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 142 - Forks: 68

chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

Language: Clojure - Size: 35.1 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 88 - Forks: 12

reslp/dockerfiles

A collection of Dockerfiles for different containers I use.

Language: Dockerfile - Size: 321 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 2 - Forks: 1

i2bc/ORFmine

ORFmine is an open-source tool for identifying and analyzing all Open Reading Frames (ORFs) in genomic data, focusing on their sequences, structures, evolution and translation activities.

Language: Python - Size: 249 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 1

tanghaibao/goatools

Python library to handle Gene Ontology (GO) terms

Language: Python - Size: 57.5 MB - Last synced: about 12 hours ago - Pushed: 19 days ago - Stars: 727 - Forks: 209

open2c/bioframe

Genomic Interval Operations on Pandas DataFrames

Language: Python - Size: 3.55 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 162 - Forks: 26

HKU-BAL/Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Language: Python - Size: 3.19 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 218 - Forks: 26

lucidrains/enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Language: Python - Size: 8.75 MB - Last synced: about 10 hours ago - Pushed: about 1 month ago - Stars: 390 - Forks: 70

HKU-BAL/ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

Language: Python - Size: 3.46 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 49 - Forks: 5

datacarpentry/genomics-workshop

Genomics Workshop Overview

Size: 71.8 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 42 - Forks: 99

datacarpentry/shell-genomics

Introduction to the Command Line for Genomics

Size: 53.8 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 59 - Forks: 188

stephaniehicks/stephaniehicks.github.io

Website for Stephanie C. Hicks

Language: JavaScript - Size: 15.8 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 0

lhqing/ALLCools

Toolkit for single-cell DNA methylation analysis.

Language: Python - Size: 282 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 33 - Forks: 13

JLSteenwyk/PhyKIT

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

Language: Python - Size: 17.4 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 47 - Forks: 6

JLSteenwyk/ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Language: Python - Size: 25.7 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 52 - Forks: 4