geneontology/go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.

Language: Python - Size: 158 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 31 - Forks: 10

eggnogdb/eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

Language: Python - Size: 94.9 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 536 - Forks: 106

xihaoli/STAARpipeline-Tutorial

The tutorial for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

Language: R - Size: 195 KB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 19 - Forks: 17

metagenopolis/meteor

Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform specie level taxonomic assignments and functional analysis.

Language: Python - Size: 67.5 MB - Last synced: 14 days ago - Pushed: 21 days ago - Stars: 6 - Forks: 0

dalmolingroup/euryale

A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA

Language: Nextflow - Size: 9 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 3 - Forks: 0

metagenome-atlas/atlas

ATLAS - Three commands to start analyzing your metagenome data

Language: Python - Size: 20.2 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 346 - Forks: 98

geneontology/noctua

Graph-based modeling environment for biology, including prototype editor and services

Language: JavaScript - Size: 192 MB - Last synced: 19 days ago - Pushed: 4 months ago - Stars: 35 - Forks: 13

geneontology/amigo

AmiGO is the public interface for the Gene Ontology.

Language: JavaScript - Size: 178 MB - Last synced: 19 days ago - Pushed: 22 days ago - Stars: 29 - Forks: 17

sigven/geneOncoX

Human gene annotations for the oncology domain

Language: R - Size: 40.6 MB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 6 - Forks: 0

meringlab/annotation_system_assessment

Snakemake pipeline to benchmark 11 functional pathway annotation systems

Language: Python - Size: 7.1 MB - Last synced: 23 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

li-lab-genetics/staarpipeline-rap

An app for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline in UK Biobank RAP

Language: R - Size: 58.6 KB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 3 - Forks: 2

xihaoli/STAARpipeline

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

Language: R - Size: 2.06 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 50 - Forks: 13

moshi4/COGclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Language: Python - Size: 29.5 MB - Last synced: 8 days ago - Pushed: 6 months ago - Stars: 39 - Forks: 5

geneontology/go-ontology

Source ontology files for the Gene Ontology

Language: Makefile - Size: 1.49 GB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 205 - Forks: 39

iquasere/reCOGnizer

A tool for domain based annotation with databases from the Conserved Domains Database

Language: HTML - Size: 61.3 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 24 - Forks: 2

iquasere/UPIMAPI

UniProt Id Mapping through API

Language: Python - Size: 9.66 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 25 - Forks: 4

geneontology/helpdesk

The Gene Ontology Helpdesk

Size: 120 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 15 - Forks: 6

pentalpha/rna_gatherer

ncRNA identification, annotation and functional prediction

Language: Python - Size: 117 MB - Last synced: about 1 month ago - Pushed: 5 months ago - Stars: 2 - Forks: 1

lucast122/MMonitor

Software for monitoring metagenomes using nanopore sequencing reads

Language: C - Size: 156 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

xihaoli/MetaSTAAR

An R package for performing MetaSTAAR procedure in whole-genome sequencing studies

Language: R - Size: 1.41 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 19 - Forks: 4

xihaoli/STAAR

An R package for performing STAAR procedure in whole-genome sequencing studies

Language: C++ - Size: 2.93 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 81 - Forks: 38

xpolak37/COGtools

A computational tools for improving the functional annotation of bacterial genomes and the classification of CDSs into cllusters of orthologous groups (COGs). It allows summarizing annotations from different resources to provide a more accurate annotation of genes regarding their assignment into COGs and their categories.

Language: Python - Size: 6.99 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

xihaoli/STAARpipelineSummary

An R package for summarizing and visualizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies generated by STAARpipeline

Language: R - Size: 962 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 5

narek01/DAVIDpy

Python3 extension for DAVID Bioinformatics Tool

Language: Python - Size: 19.5 KB - Last synced: 7 days ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

xihaoli/MultiSTAAR

An R package for performing MultiSTAAR procedure in whole-genome sequencing studies

Language: R - Size: 423 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

li-lab-genetics/favorannotator-rap

An app for automatically functionally annotating the variants of whole-genome/whole-exome sequencing (WGS/WES) studies and integrating the functional annotations with the genotype data using FAVORannotator in UK Biobank RAP

Language: R - Size: 22.5 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

xihaoli/MACIE

Multi-dimensional Annotation Class Integrative Estimation

Language: Python - Size: 42 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 8 - Forks: 1

KChen-lab/TransVar

A multi-way annotator for genetic elements and genetic variations

Language: Python - Size: 5.24 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

geneontology/paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.

Language: Java - Size: 18.6 MB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 2 - Forks: 4

schellt/maker-functional

Adjustment of MAKER's functional annotation scripts

Language: Perl - Size: 5.86 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

li-lab-genetics/staarpipelinesummary_indvar-rap

An app for summarizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies in UK Biobank RAP

Language: R - Size: 21.5 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 1

li-lab-genetics/staarpipelinesummary_varset-rap

An app for summarizing association analysis results of whole-genome/whole-exome sequencing (WGS/WES) studies in UK Biobank RAP

Language: R - Size: 31.3 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 1

geneontology/touchup

for keeping the PAINT GAF files up to date

Language: Java - Size: 74.5 MB - Last synced: 9 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 3

geneontology/gaferencer

Perform annotation deepening and satisfiability checking for GO annotations in GAFs

Language: Scala - Size: 230 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

alexjisa/TAIFA

TAIFA is a workflow for conducting Whole-Genome Sequencing (WGS) of bacteria

Size: 13.4 MB - Last synced: 5 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

Dill-PICL/GOMAP-singularity

GOMAP-Singularity is the containerized version of GOMAP

Language: Shell - Size: 35.8 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 10 - Forks: 5

Dill-PICL/GOMAP

Language: R - Size: 252 KB - Last synced: 7 months ago - Pushed: 12 months ago - Stars: 4 - Forks: 3

fhaive/nextcast

Nextcast: a software suite to analyse and model toxicogenomics data

Language: R - Size: 62.3 MB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

sagnikbanerjee15/fungal_genome_assemblies_and_annotation

Analysis workflow to generate fungal assemblies, generate gene structural and functional annotations

Language: Shell - Size: 1.11 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

geneontology/ribbon 📦

(DEPRECATED) Short form matrix view of all GO annotations for a given gene

Language: JavaScript - Size: 37.8 MB - Last synced: 9 days ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 7

fursham-h/factR

factR: Functional Annotation of Custom-assembled Transcripts in R

Language: R - Size: 12.6 MB - Last synced: 25 days ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

parfreylab/metagenome_assembly_pipeline

A pipeline to go from raw sequencing data to high quality bins and pretty plots.

Language: Python - Size: 61.5 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 7 - Forks: 5

xpolak37/the-COG-or

Package for improving the functional annotation of bacterial genomes, classification of protein-coding sequences into clusters of orthologous groups, and visualization of the final annotated genome.

Language: Python - Size: 2.69 MB - Last synced: 11 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

Bohdan-Khomtchouk/geneXtendeR

R/Bioconductor package for optimized functional annotation of ChIP-seq data

Language: R - Size: 67 MB - Last synced: 19 days ago - Pushed: about 5 years ago - Stars: 9 - Forks: 1

PatrickHallaert/FAVOR_hg19_database

A back-end functional annotation database for the hg19 reference genome inspired by the FAVOR project.

Language: Jupyter Notebook - Size: 188 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

corbinq/GAMBIT

Tool for integrative gene-based association analysis using GWAS summary stats

Language: C++ - Size: 4.55 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 8 - Forks: 5

jungsoh/transcriptomics-course

Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

Language: HTML - Size: 20.3 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

jungsoh/bioinformatics-lab-course

Material used for a bioinformatics computer lab course, covering DNA/RNA sequence assembly and analysis, phylogenetic analysis, gene functional annotation, and metagenomic analysis

Language: HTML - Size: 16 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

rbr7/compgenomics2021

Using un-assembled genome sequence data from the Centers for Disease Control and Prevention (CDC) proceed through five distinct stages of analysis and interpretation of that data: 1-genome assembly, 2-gene prediction, 3-functional annotation, 4-comparative genomics and 5-production of a predictive webserver.

Language: AMPL - Size: 48.8 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

geneontology/molecular_function_refactoring

A repository for the development of patterns and terms for axiomatisation and refactoring of the GO MF branch

Language: Python - Size: 52.7 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 1 - Forks: 1

geneontology/noctua-annotation-review

Language: JavaScript - Size: 48.9 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

geneontology/api-gorest

GitHub repository for the NodeJS/Express REST web service go-api-sparql. Used for the front-end www.geneontology.org/gocam.

Language: JavaScript - Size: 130 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

brettwhitty/bw-msu-tools

Archive of personal scripts repository from my various projects in the Buell Lab at MSU (Jan. 2008 - Apr. 2011)

Language: Perl - Size: 3.76 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0