functional-annotation | Topic | Ecosyste.ms: Repos

Topic: "functional-annotation"

eggnogdb/eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

Language: Python - Size: 94.9 MB - Last synced at: 21 days ago - Pushed at: about 1 year ago - Stars: 611 - Forks: 108

metagenome-atlas/atlas

ATLAS - Three commands to start analyzing your metagenome data

Language: Python - Size: 20.3 MB - Last synced at: about 21 hours ago - Pushed at: 7 days ago - Stars: 387 - Forks: 101

geneontology/go-ontology

Source ontology files for the Gene Ontology

Language: Makefile - Size: 1.78 GB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 231 - Forks: 40

xihaoli/STAAR

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

Language: C++ - Size: 2.94 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 91 - Forks: 42

moshi4/COGclassifier

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

Language: Python - Size: 33.6 MB - Last synced at: 3 days ago - Pushed at: 13 days ago - Stars: 65 - Forks: 6

xihaoli/STAARpipeline

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

Language: R - Size: 2.2 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 53 - Forks: 17

geneontology/noctua

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

Language: JavaScript - Size: 192 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 39 - Forks: 12

geneontology/go-annotation

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

Language: Python - Size: 158 MB - Last synced at: 4 days ago - Pushed at: 13 days ago - Stars: 38 - Forks: 10

geneontology/amigo

AmiGO is the public interface for the Gene Ontology.

Language: JavaScript - Size: 178 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 31 - Forks: 17

iquasere/UPIMAPI

UniProt Id Mapping through API

Language: Python - Size: 9.7 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 31 - Forks: 4

iquasere/reCOGnizer

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

Language: HTML - Size: 61.4 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 30 - Forks: 2

xihaoli/STAARpipeline-Tutorial

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

Language: R - Size: 251 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 26 - Forks: 17

xihaoli/MetaSTAAR

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

Language: R - Size: 1.43 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 21 - Forks: 7

geneontology/helpdesk

The Gene Ontology Helpdesk

Size: 128 KB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 16 - Forks: 6

dalmolingroup/euryale

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

Language: Nextflow - Size: 23.1 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 13 - Forks: 0

Dill-PICL/GOMAP-singularity

GOMAP-Singularity is the containerized version of GOMAP

Language: Shell - Size: 35.8 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 10 - Forks: 5

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: 1.61 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 9 - Forks: 5

Bohdan-Khomtchouk/geneXtendeR

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

Language: R - Size: 67 MB - Last synced at: about 10 hours ago - Pushed at: about 6 years ago - Stars: 9 - Forks: 1

xihaoli/MACIE

Multi-dimensional Annotation Class Integrative Estimation

Language: Python - Size: 42 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 1

corbinq/GAMBIT

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

Language: C++ - Size: 4.55 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 8 - Forks: 5

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 at: about 2 years ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 5

sigven/geneOncoX

Human gene annotations for the oncology domain

Language: R - Size: 43 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 6 - Forks: 0

MuhammadMuneeb007/EFGPP

Exploratory Framework for Genotype-Phenotype Prediction

Language: Python - Size: 14.9 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 4 - 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: 62.5 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 2

xihaoli/MultiSTAAR

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

Language: R - Size: 655 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 4 - Forks: 2

Dill-PICL/GOMAP

Language: R - Size: 252 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 3

geneontology/ribbon 📦

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

Language: JavaScript - Size: 37.8 MB - Last synced at: 10 days ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 7

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 at: 10 months ago - Pushed at: about 8 years ago - Stars: 4 - Forks: 4

li-lab-genetics/MetaSTAARlite

A lightweight R package for performing association meta-analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using MetaSTAARlite pipeline

Language: R - Size: 10.3 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 3 - Forks: 2

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: 24.4 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - 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 at: about 2 years ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

narek01/DAVIDpy

Python3 extension for DAVID Bioinformatics Tool

Language: Python - Size: 19.5 KB - Last synced at: 6 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

lucast122/MMonitor-old

Software for monitoring metagenomes using nanopore sequencing reads

Language: C - Size: 156 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 0

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

pentalpha/rna_gatherer_2020 📦

ncRNA identification, annotation and functional prediction

Language: Python - Size: 117 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

li-lab-genetics/MetaSTAARlite-Tutorial

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

Language: R - Size: 126 KB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 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

Language: R - Size: 21.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year 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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

alexjisa/TAIFA

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

Size: 13.4 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

fursham-h/factR

factR: Functional Annotation of Custom-assembled Transcripts in R

Language: R - Size: 12.6 MB - Last synced at: 17 days ago - Pushed at: almost 2 years ago - Stars: 1 - 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 at: 10 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

fhaive/nextcast

Nextcast: a software suite to analyse and model toxicogenomics data

Language: R - Size: 62.3 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

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 at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - 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 at: 10 months ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 1

KChen-lab/TransVar

A multi-way annotator for genetic elements and genetic variations

Language: Python - Size: 5.24 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

NIGMS/Transcriptome-Assembly-Refinement-and-Applications

In this module, you will learn how to use a Nextflow pipeline to assemble and annotate a novel transcriptome using RNA-seq data

Language: Jupyter Notebook - Size: 5.84 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 0 - Forks: 4

WeeYeZhi/master_logbook_web_app

This is the digital version of my master project's logbook that is created by using Streamlit Python package to document all the command lines and codes that I ran to do my project so that other researchers can later reproduce the exact same analysis results

Language: Python - Size: 421 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

geneontology/gaferencer

Perform annotation deepening and satisfiability checking for GO annotations in GAFs

Language: Scala - Size: 232 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - 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 at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

meringlab/annotation_system_assessment

Snakemake pipeline to benchmark 11 functional pathway annotation systems

Language: Python - Size: 7.1 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

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 at: 9 months ago - Pushed at: almost 3 years ago - Stars: 0 - 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 at: about 2 years ago - Pushed at: over 3 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 at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0