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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CellProfiler Image Analysis Software Resource Report Resource Website 1000+ mentions |
CellProfiler Image Analysis Software (RRID:SCR_007358) | image analysis software, software application, 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 | 2026-02-12 09:44:26 | 3265 | |||||
|
GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, portal, project 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 | 2026-02-12 09:46:06 | 7700 | |||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, software resource, data processing software | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-02-12 09:46:55 | 59 | ||||||
|
liftOver Resource Report Resource Website 500+ mentions |
liftOver (RRID:SCR_018160) | service resource, software application, software resource, data processing software | Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments. | Convert genome coordinate, genome annotation file, translate genomic coordinate, assembly version, retrieve orthologous region |
is related to: UCSC Genome Browser has parent organization: University of California at Santa Cruz; California; USA |
NHGRI ; Howard Hughes Medical Institute ; NCI |
DOI:10.1093/nar/gkj144 | Free, Available for download, Freely available | SCR_018160 | 2026-02-12 09:46:46 | 762 | ||||||||
|
mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | software application, software resource, data processing software | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth https://sources.debian.org/src/mosdepth/ |
SCR_018929 | 2026-02-12 09:46:58 | 38 | ||||||
|
ProteomeTools Resource Report Resource Website 10+ mentions |
ProteomeTools (RRID:SCR_018535) | data or information resource, portal, project 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 | 2026-02-12 09:46:53 | 21 | |||||||
|
Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | source code, software application, software resource | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-02-12 09:43:04 | 0 | |||||||
|
Hapmix Resource Report Resource Website 10+ mentions |
Hapmix (RRID:SCR_004203) | HAPMIX | source code, software application, software resource | Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, admixed, population, genotype, single nucleotide polymorphism, ancestry, chromosomal segment, snp array |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U01-HG004168; NHLBI R01-HL087699 |
PMID:19543370 | Restricted | nlx_22768, OMICS_02082 | http://www.hsph.harvard.edu/faculty/alkes-price/software/ http://www.stats.ox.ac.uk/~myers/software.html https://reich.hms.harvard.edu/software |
http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004203 | 2026-02-12 09:43:46 | 45 | ||||
|
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | data or information resource, database, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-02-12 09:43:36 | 0 | ||||||
|
BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | software application, workflow software, software resource, data processing software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NIGMS R01 GM126019; NHLBI U54 HL127624; NHGRI U24HG012674; NIAID R03AI159286 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-02-12 09:47:07 | 1 | ||||||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie https://bio.tools/stringtie https://sources.debian.org/src/stringtie/ |
SCR_016323 | 2026-02-12 09:46:47 | 4072 | ||||||
|
SVEngine Resource Report Resource Website 1+ mentions |
SVEngine (RRID:SCR_016235) | sequence analysis software, software resource, simulation software, software application, data analysis software, data processing software | Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats. | structural, alteration, clonality, NGS, simulator, gene, allele, haplotype, variant | NHGRI R01 HG006137; CNSF 61370131 |
Free, Available to download | SCR_016235 | SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator | 2026-02-12 09:46:29 | 3 | |||||||||
|
DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-02-12 09:46:42 | 2 | ||||
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miQC Resource Report Resource Website 1+ mentions |
miQC (RRID:SCR_022697) | software resource, software application, data analysis software, data processing software | Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset. | scRNA-seq data quality control, QC metric, low quality data prediction, single cell RNA-sequencing data | NCI CA237170; NHGRI HG009007; European Union Horizon 2020 research and innovation program ; Academy of Finland ; Cancer Foundation Finland |
PMID:34428202 | Free, Available for download, Freely available | SCR_022697 | 2026-02-12 09:47:27 | 2 | |||||||||
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Hetnet Connectivity Search Resource Report Resource Website 1+ mentions |
Hetnet Connectivity Search (RRID:SCR_023630) | Hetnet | software resource, web service, data access protocol | 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 | 2026-02-12 09:47:42 | 1 | |||||||
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Reactome Knowledgebase Resource Report Resource Website 100+ mentions |
Reactome Knowledgebase (RRID:SCR_023504) | data access protocol, software resource, web service, database, data or information resource | 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 | 2026-02-12 09:48:21 | 445 | |||||||||
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Michigan Imputation Server Resource Report Resource Website 1+ mentions |
Michigan Imputation Server (RRID:SCR_023554) | software resource, web service, data access protocol | 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 | 2026-02-12 09:47:56 | 8 | |||||||
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ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | software toolkit, software resource, software application, data analysis software, data processing software | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | NHGRI RM1 HG007735; NHGRI UM1 HG009442; NCI R35 CA209919; NHGRI UM1 HG009436; NCI U2C CA233311; NIAID U19 AI057266; NIA K99 AG059918; American Society of Hematology Scholar Award ; International Collaborative Award ; Defense Advanced Research Project Agency ; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR https://www.archrproject.com/ https://github.com/GreenleafLab/ArchR_2020 |
SCR_020982 | 2026-02-12 09:47:08 | 358 | ||||||||
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PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | software toolkit, software resource, software application, data analysis software, data processing software | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-02-12 09:47:46 | 8 | ||||||
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LocusZoom.org Resource Report Resource Website 10+ mentions |
LocusZoom.org (RRID:SCR_021374) | software resource, web service, data access protocol | Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. | Generate interactive plots, shareable plots, GWAS summary statistics, visualizing statistical genetic data, genetic association study | NHGRI HG009976; NIH BOEH15AMP |
DOI:10.1093/bioinformatics/btab186 | Free, Freely available | SCR_021374 | LocusZoom.js | 2026-02-12 09:47:17 | 32 |
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