functional-annotation

There are 3 repositories under functional-annotation topic.

• eggnogdb / eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

  annotationsorthology-assignmentsfunctional-annotationgenomics
  Language:Python 537

• metagenome-atlas / atlas

  ATLAS - Three commands to start analyzing your metagenome data

  metagenomicsannotationsnakemakeassemblygenomic-binningfunctional-annotationtaxonomic-classifications
  Language:Python 349
• go-ontology

  geneontology / go-ontology

  Source ontology files for the Gene Ontology

  functional-annotationgene-ontologygeneontologygooboobofoundryontologyowl
  Language:Makefile 207

• xihaoli / STAAR

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

  whole-genome-sequencingstatistical-geneticsstaar-procedurefunctional-annotationrare-variant-analysis
  Language:C++ 84

• xihaoli / STAARpipeline

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

  statistical-geneticswhole-genome-sequencingwhole-exome-sequencingfunctional-annotationrare-variant-analysisstaar-pipeline
  Language:R 51
• COGclassifier

  moshi4 / COGclassifier

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

  pythonbioinformaticscoggenomicsfunctional-annotationfunctional-analysiscomparative-genomicsvisualizationproteinmicrobial-genomicsgenome-analysis
  Language:Python 40

• geneontology / noctua

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

  noctuaowlgo-camgeneontologypathwayscurationontologynoctua-modelsfunctional-annotationannotation
  Language:JavaScript 35

• geneontology / go-annotation

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

  annotationgeneontologycurationontologyfunctional-annotationgenesannotations
  Language:Python 31

• geneontology / amigo

  AmiGO is the public interface for the Gene Ontology.

  geneontologyannotationsontologybrowsergenesfunctional-annotation
  Language:JavaScript 29

• iquasere / reCOGnizer

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

  cog-assignmentannotationproteinfastaquantificationgenomicsfunctional-annotation
  Language:HTML 27

• iquasere / UPIMAPI

  UniProt Id Mapping through API

  genomicsuniprotid-mappingfunctional-informationtaxonomic-informationfunctional-annotation
  Language:Python 26

• xihaoli / MetaSTAAR

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

  statistical-geneticswhole-genome-sequencingmeta-analysisfunctional-annotationrare-variant-analysismetastaar-procedure
  Language:R 20

• xihaoli / STAARpipeline-Tutorial

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

  statistical-geneticswhole-exome-sequencingwhole-genome-sequencingfunctional-annotationrare-variant-analysisstaar-pipeline
  Language:R 19

• geneontology / helpdesk

  The Gene Ontology Helpdesk

  geneontologyontologyontologieshelpdeskfunctional-annotationnoctuanoctua-modelsgenescurationgene-ontologygo
  15

• corbinq / GAMBIT

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

  gwasgwas-summary-statisticsgene-basedgenetic-analysistwasintegrative-analysisfunctional-annotationgenetic-epidemiologyregulatory-elements
  Language:C++ 11

• Dill-PICL / GOMAP-singularity

  GOMAP-Singularity is the containerized version of GOMAP

  functional-annotationgene-ontologysingularity
  Language:Shell 11

• Bohdan-Khomtchouk / geneXtendeR

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

  chip-seqcomputational-biologyfunctional-annotationbioinformaticsepigeneticscrbioconductor
  Language:R 9

• parfreylab / metagenome_assembly_pipeline

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

  pythonbashmetagenomicsassemblyilluminafunctional-annotationrquality-controlpipeline
  Language:Python 9

• xihaoli / MACIE

  Multi-dimensional Annotation Class Integrative Estimation

  functional-annotationgeneticsbioinfomaticsintegrative-scores
  Language:Python 9

• xihaoli / STAARpipelineSummary

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

  statistical-geneticswhole-genome-sequencingwhole-exome-sequencingfunctional-annotationrare-variant-analysisstaar-pipeline
  Language:R 8
• meteor

  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.

  metagenomicstaxonomic-classificationfunctional-annotationstrain-profiling
  Language:Python 6

• sigven / geneOncoX

  Human gene annotations for the oncology domain

  annotationscancer-genomicscancer-researchdriver-genesgenegene-panelsoncogenestumor-suppressor-genesfunctional-annotation
  Language:R 6

• sagnikbanerjee15 / fungal_genome_assemblies_and_annotation

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

  functional-annotationgene-annotationgenome-assembly
  Language:Shell 5

• Dill-PICL / GOMAP

  functional-annotationgene-ontology
  Language:R 4

• 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.

  geneontologycurationannotation-toolannotationontologyfunctional-annotationpaintgenephylogeneticsorthologyowl
  Language:Java 4

• geneontology / ribbon

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

  geneontologyfunctional-annotationannotations
  Language:JavaScript 4

• dalmolingroup / euryale

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

  diamondfunctional-annotationkaijumetagenomicstaxonomic-classificationnextflowpipelinesnakemake
  Language:Nextflow 3

• jungsoh / transcriptomics-course

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

  annotation-datade-novo-assemblydifferential-expression-analysisfunctional-annotationtranscriptome-annotationtranscriptome-assemblytranscriptomics
  Language:HTML 3

• 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

  functional-annotationstaar-pipelinestatistical-geneticswhole-exome-sequencingwhole-genome-sequencing
  Language:R 3

• narek01 / DAVIDpy

  Python3 extension for DAVID Bioinformatics Tool

  bioinformaticsbioinformatics-tooldavidfunctional-annotationpython
  Language:Python 3

• xihaoli / MultiSTAAR

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

  functional-annotationmulti-trait-analysismultistaar-procedurerare-variant-analysisstatistical-geneticswhole-genome-sequencing
  Language:R 3

• 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

  functional-annotationwhole-exome-sequencingwhole-genome-sequencingfavor-annotator
  Language:R 2

• pentalpha / rna_gatherer_2020

  ncRNA identification, annotation and functional prediction

  bioinformaticsbioinfoncrnafunctional-predictiongene-functionfunctional-annotationgene-predictionncrna-protein-interactionslncrnalncrna-pipelinegene-annotationpipeline
  Language:Python 2

• 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.

  bacterial-genomesbioinformaticsfunctional-annotation
  Language:Python 2

• alexjisa / TAIFA

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

  genomicsbacteriabioinformatics-pipelinecondadata-miningfunctional-annotationilluminanext-generation-sequencingpaired-endshort-readswhole-genome-sequencingstructural-annotation
  1

• 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

  functional-annotationstaar-pipelinestatistical-geneticswhole-exome-sequencingwhole-genome-sequencing
  Language:R 1