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57 search results found
Cs Video Courses
⭐
62,887
List of Computer Science courses with video lectures.
Biostar Central
⭐
563
Biostar Q&A
Hh Suite
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429
Remote protein homology detection suite.
Postgui
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335
A React web application to query and share any PostgreSQL database.
Awesome Cancer Variant Databases
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284
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
Kaiju
⭐
236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Krakenuniq
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201
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Artemis
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191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Docker Builds
⭐
158
📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
Genome_updater
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123
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Vdjdb Db
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122
🗂️ [vdjdb.cdr3.net is down for maintenance] Git-based TCR database storage & management. Submissions welcome!
Bio4j
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112
Bio4j abstract model and general entry point to the project
Run_dbcan
⭐
109
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
Geoparse
⭐
98
Python library to access Gene Expression Omnibus Database (GEO)
Terpene Profile Parser For Cannabis Strains
⭐
93
Parser and database to index the terpene profile of different strains of Cannabis from online databases
Referenceseeker
⭐
85
Rapid determination of appropriate reference genomes.
Bget
⭐
84
Portable command-line tool to query bioinformatics APIs, data, databases and files.
Staramr
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75
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Goenrich
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68
GO enrichment with python -- pandas meets networkx
Bonsai
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68
Bonsai: Fast, flexible taxonomic analysis and classification
Kmer Db
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68
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
Chip Atlas
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61
ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser
Uta
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59
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
Bigsdb
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53
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Bioinstaller
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50
A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
Metacache
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49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Ensembl Compara
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46
The Ensembl Compara Perl API and SQL schema
Microbiomebestpracticereview
⭐
45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Mmseqs2 App
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44
MMseqs2 app to run on your workstation or servers
Taxadb
⭐
32
🐣 locally query the ncbi taxonomy
Locuszoom Standalone
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30
Create regional association plots from GWAS or meta-analysis
Bioqueue
⭐
28
A novel pipeline framework to accelerate bioinformatics analysis
Stringmlst
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27
Fast k-mer based tool for multi locus sequence typing (MLST)
Bridgedb
⭐
26
The BridgeDb Library source code
Rnacentral Webcode
⭐
25
RNAcentral website source code
Socru
⭐
23
Order and orientation of complete bacterial genomes
Vdjmatch
⭐
22
Matching T-cell repertoire against a database of TCR antigen specificities
Pubdata
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21
Smart search engine for all bioinformatics databases worldwide
Cmdbtools
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21
Command line tools for CMDB varaints browser
Immunedb
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19
ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
Super Focus
⭐
19
A tool for agile functional analysis of shotgun metagenomic data
Pipetaxon
⭐
18
PipeTaxon exposes the ncbi taxonomy database as a REST API.
Matam
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18
Mapping-Assisted Targeted-Assembly for Metagenomics
Entrez
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16
A simple Python interface to the NCBI databases (Entrez).
Mlst_check
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14
Multilocus sequence typing by blast using the schemes from PubMLST
Virmet
⭐
13
Set of tools for viral metagenomics.
Streamformatics
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13
Real-time species-typing visualisation for nanopore data.
Genomehubs
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12
Search and explore genomic metadata, Earth BioGenome Project progress and assembly features
Efp Seq_browser
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12
An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.
Msigdb
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11
Molecular Signatures Database as a list
Biodwh2
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10
BioDWH2 is an easy-to-use, automated, graph-based data warehouse and mapping tool for bioinformatics and medical informatics.
Sequence Database Curator
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10
This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
Pathway Forte
⭐
10
A Python package for benchmarking pathway database with functional enrichment and classification methods
Cazy_webscraper
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10
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
Xgt
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9
Efficient and fast querying and parsing of GTDB's data
Subsystems
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8
Code for making bioinformatics work with the SEED subsystems database a little easier.
Biochempantry
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8
Load bioinformatics datasets into a local database
Db.rna16s
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8
A comprehensive, compact, and automatically curated 16S database
Ipdmhc
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8
Github for files currently published in the IPD-MHC FTP Directory hosted at the European Bioinformatics Institute
Seal
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8
SEAL db - Simple, Efficient And Lite database for NGS
Protocols
⭐
7
protocols for bioinformatics data analysis
Dbsnp Pg
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7
PostgreSQL schema for NCBI dbSNP
Biolink
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6
🔗 R package for creating hyperlinks to biological databases and resources
Covsonar
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6
A database-driven system for handling genomic sequences of SARS-CoV-2 and screening genomic profiles.
Rfam Website
⭐
5
Rfam website source code
Results
⭐
5
Results of the evaluation of pathway databases using TCGA datasets
Odg
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5
ODG: Omics Database Generator - Integration toolkit for -omics data
Tachyon
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5
Wikigenomesbase
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5
A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.
Clinical_variant_database
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5
Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensembl dataset. Originally developed as part of a Masters in Bioinformatics project @ University of Exeter
Csurvival
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5
cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines
Ps4 Dataset
⭐
5
The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.
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