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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CellProfiler Image Analysis Software Resource Report Resource Website 1000+ mentions |
CellProfiler Image Analysis Software (RRID:SCR_007358) | software application, image analysis software, software resource, data processing software | Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types. | high-throughput, high content imaging, software, image, cell, phenotype, measurement, subcellular, intensity, size, shape, analysis, algorithm |
is listed by: Debian is related to: CellProfiler Analyst has parent organization: Broad Institute |
NIGMS R01 GM089652; NIGMS RC2 GM092519; NHGRI RL1 HG004671 |
PMID:21349861 PMID:17076895 PMID:19014601 PMID:19188593 |
Free, Available for download, Freely available | SCR_010649, nlx_66812, nif-0000-00280 | https://sources.debian.org/src/cellprofiler/ | SCR_007358 | Cell Profiler, CellProfiler - cell image analysis software | 2026-07-28 09:41:45 | 3265 | |||||
|
GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | project portal, data or information resource, portal, dataset | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-07-28 09:43:38 | 7700 | |||||
|
ProteomeTools Resource Report Resource Website 10+ mentions |
ProteomeTools (RRID:SCR_018535) | project portal, data or information resource, portal | Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research. | Molecular tool, human proteome, proteome, human, peptide, data |
is related to: ProteomicsDB is related to: ProteomeXchange |
German Federal Ministry of Education and Research ; Alexander von Humboldt Foundation ; American Recovery and Reinvestment Act ; NHGRI RC2 HG005805; NIGMS R01 GM087221; NCRR S10 RR027584; NIGMS P50 GM076547; European Research Council ; Swiss National Science Foundation |
PMID:28135259 | Free, Freely available | http://www.proteometools.org | SCR_018535 | 2026-07-28 09:44:46 | 21 | |||||||
|
GeneTests Resource Report Resource Website 10+ mentions |
GeneTests (RRID:SCR_010725) | GeneTests | service resource, biomaterial analysis service, narrative resource, data or information resource, database, production service resource, material analysis service, analysis service resource, topical portal, portal, training material | The GeneTests Web site, a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, is available at no cost to all interested persons. By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making. At This Site: * GeneReviews: Expert-authored peer-reviewed disease descriptions * Laboratory Directory: International directory of genetic testing laboratories * Clinic Directory: International directory of genetics and prenatal diagnosis clinics * Educational Materials: Illustrated glossary, information on genetic services, PowerPoint presentations, annotated Internet resources We comply with the HONcode standard for trustworthy health information. |
has parent organization: University of Washington; Seattle; USA has parent organization: NCBI |
NCI ; NHGRI 1 P41 LM/HG 06029; NLM 1 P41 LM/HG 06029; NLM contract N01-LM-4-3505; NLM 5 P41 LM07242; NLM 2 P41 LM 06001; DOE DE-FG03-02ER63301/A00 |
nlx_94696 | SCR_010725 | GeneTests: Clinical Genetic Information Resource | 2026-07-28 09:42:58 | 12 | ||||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | software application, software resource, data analysis software, data processing software | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-07-28 09:43:12 | 1325 | ||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software application, data analysis software, software resource, data management software, data processing software, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-07-28 09:44:11 | 324 | ||||||
|
Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | software application, software resource, data processing software, alignment software, image analysis software | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-07-28 09:44:02 | 2 | |||||||
|
AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | software application, source code, software resource, data processing software, alignment software, image analysis software | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NSF EF 03-31494; NHGRI R01 HG2362; NSF CCF0347992 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-07-28 09:44:01 | 388 | ||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-07-28 09:44:10 | 81 | ||||||
|
fermi-lite Resource Report Resource Website 1+ mentions |
fermi-lite (RRID:SCR_016112) | software application, algorithm resource, software resource, data processing software, alignment software, standalone software, image analysis software | Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling. | assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, calling | is related to: Illumina | NHGRI U54 HG003037; NIGMS GM100233 |
PMID:26220959 | Free, Available for download | SCR_016112 | FermiKit, Fml-asm | 2026-07-28 09:44:05 | 4 | |||||||
|
AbundantOTU+ Resource Report Resource Website 1+ mentions |
AbundantOTU+ (RRID:SCR_016527) | AbundantOTU | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset. | pyrosequencing, 16S, rRNA, gene, operational, taxonomic, unit, abundant, species, dataset |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
NHGRI R01 HG004908; NHLBI U01 HL09896001 |
PMID:22102981 | Free, Available for download, Freely available | SCR_016527 | AbundantOTU:Abundant Operational Taxonomic Unit, Abundant OTU, AbundantOTU+ | 2026-07-28 09:44:16 | 1 | ||||||
|
Reactome Knowledgebase Resource Report Resource Website 100+ mentions |
Reactome Knowledgebase (RRID:SCR_023504) | data or information resource, database, data access protocol, software resource, web service | Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis. | signaling and metabolic molecules relations, biological pathways and processes, intermediary metabolism, signaling, transcriptional regulation, apoptosis, disease | NHGRI U24 HG012198 | Free, Freely available | SCR_023504 | Reactome | 2026-07-28 09:45:56 | 445 | |||||||||
|
Michigan Imputation Server Resource Report Resource Website 1+ mentions |
Michigan Imputation Server (RRID:SCR_023554) | software resource, data access protocol, web service | Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4. | Genotype imputation, whole genotype imputation workflow, parallelization of computationally intensive tasks, | is related to: MINIMAC | NHGRI HG007022; NHLBI HL117626; NHGRI HG000376; NIDA R01DA037904; Austrian Science Fund ; European Community Seventh Framework Programme ; NIA |
PMID:27571263 | Free, Freely available | https://github.com/genepi/imputationserver | SCR_023554 | 2026-07-28 09:45:56 | 8 | |||||||
|
Hetnet Connectivity Search Resource Report Resource Website 1+ mentions |
Hetnet Connectivity Search (RRID:SCR_023630) | Hetnet | software resource, data access protocol, web service | Web app that allows users to search for the most important paths connecting any two nodes in Hetionet. | Hetionet, paths connection, paths search, paths connecting any two nodes in Hetionet, | Pfizer Inc ; NHGRI T32 HG000046; NHGRI R01 HG010067; NCI R01 CA237170; Gordon and Betty Moore Foundation |
PMID:36711546 | Free, Freely available | SCR_023630 | , Heterogeneous network Connectivity Search, heterogeneous network | 2026-07-28 09:45:59 | 1 | |||||||
|
eXpress Resource Report Resource Website 100+ mentions |
eXpress (RRID:SCR_006873) | eXpress | software application, data analysis software, sequence analysis software, software resource, data processing software |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018. From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/. Software for streaming quantification for high-throughput DNA/RNA sequencing. Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them. |
quantification, high-throughput, DNA, RNA, sequencing, target, fragment, analysis |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at Berkeley; Berkeley; USA |
NSF ; NHGRI R01HG006129 |
DOI:10.1038/nmeth.2251 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015990, OMICS_01275 | https://sources.debian.org/src/berkeley-express/ | SCR_006873 | eXpress - Streaming quantification for high-throughput sequencing, Berkeley-express | 2026-07-28 09:41:44 | 494 | ||||
|
LINCS Project Resource Report Resource Website 10+ mentions |
LINCS Project (RRID:SCR_016486) | LINCS | data or information resource, organization portal, project portal, database, consortium, portal | Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center. | data integration, network biology, gene expression, L1000, MCF10A, MEMA, P100, LINCS program, LINCS project, systems biology, systems pharmacology, FASEB list |
is related to: Drug Gene Budger is related to: LINCS Joint Project - Breast Cancer Network Browser is related to: piNET |
cancer, heart disease, neurodegenerative disorder | NIH Common Fund ; NHLBI U54 HL127624; NHLBI U54 HL127366; NHLBI U54 HL127365; NHGRI U54 HG008100; NHGRI U54 HG008097; NHGRI U54 HG008098; NINDS U54 NS091046 |
PMID:29199020 | Free, Freely available | SCR_016487 | SCR_016486 | LINCS, Library of Integrated Network based Cellular Signatures, LINCS Program | 2026-07-28 09:44:19 | 43 | ||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | software application, data analysis software, software resource, data processing software, software toolkit | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | bioBakery, biobakery | 2026-07-28 09:44:18 | 13 | |||||
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Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-07-28 09:44:26 | 20 | ||||||
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | software application, data analysis software, software resource, data processing software, network analysis software | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
European Research Council ; Research Council of Norway ; Bergen Research Foundation ; NIGMS U54 GM114833; NHGRI U41 HG003751 |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher | SCR_016759 | 2026-07-28 09:44:26 | 1 | ||||||
|
GenomicFeatures Resource Report Resource Website 50+ mentions |
GenomicFeatures (RRID:SCR_016960) | software application, data analysis software, software resource, data processing software, software toolkit | Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database. | making, manipulating, transcript, centric, annotation, genomic, location, exon, cds, bio.tools |
is used by: riboWaltz is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicfeatures | https://bio.tools/genomicfeatures | SCR_016960 | 2026-07-28 09:44:30 | 65 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
