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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | data processing software, software application, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-09-12 01:01:04 | 39 | ||||||
|
mosdepth Resource Report Resource Website 50+ mentions |
mosdepth (RRID:SCR_018929) | data processing software, software application, software resource | 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 |
NCI U24 CA209999; NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-09-12 01:01:08 | 56 | ||||||
|
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 |
Alexander von Humboldt Foundation ; American Recovery and Reinvestment Act ; European Research Council ; German Federal Ministry of Education and Research ; NCRR S10 RR027584; NHGRI RC2 HG005805; NIGMS P50 GM076547; NIGMS R01 GM087221; Swiss National Science Foundation |
PMID:28135259 | Free, Freely available | http://www.proteometools.org | SCR_018535 | 2026-09-12 01:01:07 | 23 | |||||||
|
GlyGen Resource Report Resource Website 10+ mentions |
GlyGen (RRID:SCR_023438) | data or information resource, portal, project portal | Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression. | Gly-glycobiology Gen-information, glycobiology, glycans molecular properties, glycans biophysical properties, glycans functional properties properties, glycans, genes, proteins, lipids, pathways and ontologies, data, mutation and expression data, carbohydrate and glycoconjugate related data, | NIGMS 1U01GM125267; NIGMS R24 GM146616 |
PMID:31616925 PMID:32324859 |
Free, Freely available | SCR_023438 | GlyGen Portal | 2026-09-12 01:01:12 | 20 | ||||||||
|
zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NHGRI HG006431; NIDA DA14546; NIGMS GM63904 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-09-12 01:02:36 | 4 | ||||
|
rMATS Resource Report Resource Website 10+ mentions |
rMATS (RRID:SCR_023485) | software resource | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | detection of differential alternative splicing, replicate RNA-Seq data, analysis of paired and unpaired replicates, clinical RNA-Seq datasets, genome studies, | Alfred Sloan Research Fellowship ; NIEHS R01ES024995; NIGMS R01GM088342; NIGMS R01GM105431; NINDS R01NS076631; NSF DMS1055286; NSF DMS1310391 |
PMID:25480548 | Free, Available to download, Freely available | SCR_023485 | 2026-09-12 01:00:39 | 22 | |||||||||
|
SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | data access protocol, software resource, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship ; NCI 1R33CA212697; NIGMS 5T32GM080177 |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/, https://github.com/AllonKleinLab/SPRING_dev | SCR_023578 | 2026-09-12 01:00:40 | 26 | |||||||
|
Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | data access protocol, software resource, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-09-12 01:00:40 | 16 | |||||||
|
MicrobeJ Resource Report Resource Website 1+ mentions |
MicrobeJ (RRID:SCR_023914) | data analysis software, data processing software, image processing software, software application, software resource | Software tool for high throughput bacterial cell detection and quantitative analysis. Used to analyze bacterial cells. Used to process images derived from variety of microscopy experiments with special emphasis on large image sets. Performs intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci, and organelles, determines their sub-cellular localization with sub-pixel resolution, and tracks them over time. | bacterial cell detection, analyze bacterial cells, bacteria quantitative analysis, process images, intensity and morphology measurements, | is a plug in for: ImageJ | Indiana University Office of the Vice President for Research ; NCATS UL1TR001108; NIGMS GM113172; NIGMS GM51986 |
PMID:27572972 | Free, Available for download, Freely available | SCR_023914 | 2026-09-12 01:00:44 | 9 | ||||||||
|
microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | Austrian Science Fund ; German Research Foundation ; Korean Government ; Mexican National Council of Science and Technology ; NIAID R01AI167860; NIA U19AG063744; NIDDK T32DK007202; NIDDK U01DK119702; NIDDK U24DK133658; NIGMS 1DP2GM137413; NIGMS 1R01GM132649; NIGMS R01GM107550; NIGMS R35GM142938; NIH Office of the Director S10 OD021750; NLM 1R01LM013115; NSF ; Research Council of Norway ; Sao Paulo Research Foundation |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-09-12 01:00:50 | 7 | ||||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R01 GM061867; NIGMS R35 GM118078 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-09-12 01:00:21 | 979 | |||||||
|
ConnecTF Resource Report Resource Website 1+ mentions |
ConnecTF (RRID:SCR_022577) | data access protocol, software resource, web service | Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation. | integrate transcription factor gene interactions, validate regulatory networks, gene regulatory network validation | NIGMS F32GM116347; NIGMS RO1-GM121753; NSF PGRP IOS-1339362; NSF PGRP IOS-1840761 |
PMID:33631799 | Free, Available for download, Freely available | https://github.com/coruzzilab/connectf_server | SCR_022577 | 2026-09-12 01:00:27 | 7 | ||||||||
|
nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | data processing software, image processing software, software application, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; Multidisciplinary University Research Initiative Army Research Office ; NIAID R01AI130303; NIGMS F31GM116517; NIGMS P41GM10371; NIH Office of the Director DP2OD006514; NIMH P50MH09427; NIMH R01MH110932; NINDS R01NS076467; NINDS R01NS095367; NINDS U01NS090449; NSF NSF-1707316 |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-09-12 01:00:32 | 0 | ||||||||
|
APA-Scan Resource Report Resource Website |
APA-Scan (RRID:SCR_022974) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data. | annotated and potential alternative polyadenylation events, gene downstream 3'-UTR, RNA-seq and 3'-end-seq data, two different biological conditions, polyadenylation events | NIDDK DK097771; NIGMS R01GM113952; NSF FET2003749 |
PMID:36171568 | Free, Available for download, Freely available | SCR_022974 | 2026-09-12 01:00:31 | 0 | |||||||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | software resource, web application | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NCI U24CA224260; NHLBI U54HL127624; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-09-12 01:00:36 | 193 | |||||||
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Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
DOE CSGF fellowship ; NIGMS R01 GM106303; NSF GRFP DGE1144152 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | EVcouplings | 2026-09-12 12:59:05 | 26 | |||||
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DE-Sim Resource Report Resource Website |
DE-Sim (RRID:SCR_018770) | simulation software, software application, software resource | Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models. | Object oriented, discrete event simulation, data driven modeling, oriented discrete event simulation, computation model simulation |
is related to: NumPy is related to: SciPy is related to: Pandas is related to: SIMULA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Icahn Institute for Data Science and Genomic Technology ; NIGMS R35 GM119771; NSF 1649014 |
Free, Available for download, Freely available | SCR_018770 | Discrete Event Simulation, object oriented Discrete Event-Simulation tool | 2026-09-12 12:59:05 | 0 | ||||||||
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, data processing software, software application, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
Berlin Institute for Medical Systems Biology ; NIGMS R01 GM104962 |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-09-12 12:59:06 | 8 | ||||||
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Ascidian Stock Center (ASC) Resource Report Resource Website 1+ mentions |
Ascidian Stock Center (ASC) (RRID:SCR_014949) | ASC | biomaterial supply resource, material resource, organism supplier | Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB). | ascidian, model organism, ciona, embryology, marine organism, culturing facility | is hosted by: University of California at Santa Barbara; California; USA | NIGMS R24GM07504 | Acknowledgement requested | SCR_014949 | Ascidian Stock Center | 2026-09-12 12:58:23 | 1 | |||||||
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Caenorhabditis elegans Natural Diversity Resource (CeNDR) Resource Report Resource Website 10+ mentions |
Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) | CeNDR | biomaterial supply resource, material resource, organism supplier | Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery. | c. elegans, caenorhabditis elegans, strains, n2, roundworm, nematode, gene analysis, organism supplier, portal | has parent organization: Northwestern University; Illinois; USA | American Cancer Society Research Scholar Award ; Amazon Web Services Research Grant ; Weinberg College of Arts and Sciences starter innovation award ; Northwestern University Start-up Funds ; NIGMS R01GM107227; NSF DGE-1324585 |
PMID:27701074 | Available to the research community | SCR_014958 | Caenorhabditis elegans Natural Diversity Resource | 2026-09-12 12:58:23 | 25 |
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