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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software resource, software toolkit | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-09-05 06:32:21 | 31 | ||||||||
|
Cross Validation Resource Report Resource Website |
Cross Validation (RRID:SCR_000702) | service resource, training service resource | A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation. | model, modeling, training, data, holdout, k fold, cross, validation | has parent organization: Carnegie Mellon University; Pennsylvania; USA | nlx_19901 | SCR_000702 | 2026-09-05 06:32:22 | 0 | ||||||||||
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Montana State University Bioinformatics Core Facility Resource Report Resource Website |
Montana State University Bioinformatics Core Facility (RRID:SCR_009937) | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research. | nucleic, acid, microarray, assay, database, development, analysis, genome, assembly, pathway, data, gene, expression, metagenomics |
is listed by: Eagle I has parent organization: Montana State University |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156405 | http://cores.montana.edu/bioinformatics/ | SCR_009937 | , Montana State University, core facility, MSU, Bioinformatics Core Laboratory | 2026-09-05 06:33:37 | 0 | |||||||
|
Wistar Bioinformatics Core Facility Resource Report Resource Website |
Wistar Bioinformatics Core Facility (RRID:SCR_010203) | BCF, WI, WI BCF | access service resource, core facility, service resource | Core provides High Throughput Data Analysis, Customized Bioinformatics Services, Custom Programming, High Performance Computing, Data management. Located in the Center for Systems and Computational Biology. Provides Cancer Center investigators with database management, software application support, expertise in statistical analyses and computational modeling of biomedical research data. | Bioinformatics Facility, Wistar, mass spectrometry, data analysis, genotyping, protein expression profiling, rna, sequencing, chip-chip, assay, bioinformatics analysis, non-web programming, database development, grid computing, data, Jmanagement, storage |
is listed by: Eagle I is listed by: ABRF CoreMarketplace has parent organization: Wistar Institute |
Open | ABRF_2803, nlx_156682 | https://coremarketplace.org/?FacilityID=2803&citation=1 | https://wistar.org/our-science/shared-facilities/bioinformatics-facility, http://eagle-i.itmat.upenn.edu/i/00000138-7c98-bfbf-fbab-3b8480000000 | SCR_010203 | Bioinformatics Core, Bioinformatics Core Facility | 2026-09-05 06:33:43 | 0 | |||||
|
Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | data processing software, software application, software resource | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-09-05 06:30:47 | 7582 | ||||||
|
Apache Spark Resource Report Resource Website 10+ mentions |
Apache Spark (RRID:SCR_016557) | data analytics software, data processing software, software application, software resource | Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework. | unified, analytics, engine, large, scale, data, processing |
is related to: VariantSpark is related to: spark-xml is related to: spark-xml-utils is related to: SparkFHE has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1145/2934664 | Free, Available for download, Freely available | SCR_016557 | 2026-09-05 06:30:51 | 43 | |||||||||
|
Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | data processing software, software application, software resource | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/, https://pypi.org/project/fbprophet/ | SCR_017083 | Prophet Automatic Forecasting Procedure | 2026-09-05 06:30:52 | 3 | |||||||
|
Data Biosphere Resource Report Resource Website 1+ mentions |
Data Biosphere (RRID:SCR_016154) | data or information resource, portal, project portal | Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations. | data, environment, biomedicine, standard, module, community | Freely available | https://github.com/databiosphere/ | SCR_016154 | 2026-09-05 06:30:51 | 1 | ||||||||||
|
Stanford Center for Reproducible Neuroscience Resource Report Resource Website |
Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) | data or information resource, organization portal, portal | Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects. | computing, tools, neuroscience, data, analyze, reproducibility, fMRI, OpenfMRI, OpenNeuro, Neurovault |
has parent organization: Stanford University; Stanford; California is parent organization of: OpenNeuro is parent organization of: OpenNeuro is parent organization of: NeuroVault |
SCR_016684 | 2026-09-05 06:30:52 | 0 | |||||||||||
|
atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | data processing software, software application, software resource | Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes. | normalization, bootstrap, bayes, factor, test, reference, design, seq, count, capture, data | Gatsby Charitable Foundation ; Marie Curie 656243 |
Free, Available for download, Tutorial available | SCR_016286 | 2026-09-05 06:30:51 | 2 | ||||||||||
|
Slingshot Resource Report Resource Website 100+ mentions |
Slingshot (RRID:SCR_017012) | data processing software, software application, software resource | Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics. | identify, characterize, continuous, developmental, trajectory, single, cell, data, lineage, pseudotime, inference, transcriptomic | is used by: Totem | California Institute of Regenerative Medicine ; NCRR S10 RR029668; NHGRI T32 HG000047; NIA K01 AG045344; NIDCD R01 DC007235; NIMH U01 MH105979; Siebel Foundation |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | 2026-09-05 06:30:52 | 102 | ||||||||
|
imctools Resource Report Resource Website 10+ mentions Rating or validation data |
imctools (RRID:SCR_017132) | IMCtools | data processing software, software application, software resource | Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc. | preprocessing, pipeline, imaging, mass, cytometry, data, convert, IMC, raw, file, TIFF |
has parent organization: University of Zurich; Zurich; Switzerland is a plug in for: Fiji |
European Research Council ; NIDDK UC4 DK108132; PhosphonetPPM and MetastasiX SystemsX grant ; Roche Postdoctoral Fellowship ; SNSF Assistant Professorship grant ; Swiss National Science Foundation |
PMID:29605184 | Free, Available for download, Freely available | https://bodenmillergroup.github.io/imctools/build/html/index.html | SCR_017132 | imaging mass spectrometry tools | 2026-09-05 06:30:52 | 25 | |||||
|
NMF Toolbox Resource Report Resource Website 1+ mentions |
NMF Toolbox (RRID:SCR_017069) | data processing software, software application, software resource | Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach. | non negative, matrix, factorization, variant, coefficient, data, mining, bioinformatics |
is related to: MATLAB is related to: Algorithms and Framework for Nonnegative Matrix Factorization has parent organization: University of Southern California; Los Angeles; USA |
Free, Available for download, Freely available | https://sites.google.com/site/nmftool/, https://sail.usc.edu/~cvaz/nmftoolbox.html | SCR_017069 | NMF MATLAB Toolbox, Non-negative Matrix Factorization toolbox, Non negative Matrix Factorization Toolbox, NMF Toolbox | 2026-09-05 06:30:52 | 4 | ||||||||
|
Inxight Resource Report Resource Website 10+ mentions |
Inxight (RRID:SCR_016490) | data or information resource, database, organization portal, portal | Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use. | drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, use | NIH | Free, Freely available | SCR_016490 | 2026-09-05 06:30:51 | 16 | ||||||||||
|
NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | data or information resource, organization portal, portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels, https://github.com/elixir-no-nels/nels-core, https://bio.tools/nels | SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-09-05 06:30:51 | 3 | |||||
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AssayZap Resource Report Resource Website 10+ mentions |
AssayZap (RRID:SCR_016991) | data processing software, software application, software resource | Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order. | assay, calculator, RIA, ELISA, IRMA, Biosoft, data, process | Commercially available | SCR_016991 | 2026-09-05 06:30:52 | 15 | |||||||||||
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Scmap Resource Report Resource Website 10+ mentions |
Scmap (RRID:SCR_017338) | data processing software, software application, software resource | Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments. | Unsupervised, projection, single, cell, RNA-seq, data |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:29608555 | Free, Available for download, Freely available | http://bioconductor.org/packages/scmap/, https://www.sanger.ac.uk/science/tools/scmap | SCR_017338 | 2026-09-05 06:30:53 | 17 | ||||||||
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ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | data processing software, software application, software resource | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-09-05 06:30:51 | 1 | ||||
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NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | data processing software, software application, software resource | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-09-05 06:30:52 | 331 | |||||||||
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ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software application, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-09-05 06:30:52 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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