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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Examl Resource Report Resource Website 50+ mentions |
Examl (RRID:SCR_016087) | Examl | software application, source code, software resource | Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers. | phylogenetic, analysis, database, large scale, whole genome, whole transcriptome, alignment, efficiency, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Heidelberg Institute for Theoretical Studies | PMID:25819675 | Free, Available for download | OMICS_08024, biotools:ExaML | https://bio.tools/ExaML https://sources.debian.org/src/examl/ |
SCR_016087 | Examl:Exascale Maximum Likelihood | 2026-02-15 09:21:46 | 60 | ||||
|
Mini Analysis Program Resource Report Resource Website 1000+ mentions |
Mini Analysis Program (RRID:SCR_002184) | Mini Analysis | software application, data processing software, data analysis software, software resource | Software tool that detects peaks of any type, any shape, any direction, and any size for neuroscientists who are studying spontaneous activities. Allows detection of virtually any kind of peaks including spontaneous miniature synaptic currents and potentials, action potential spikes, calcium imaging peaks, amperometric peaks, ECG peaks etc. It includes the complex and multiple peak detection algorithm. Has post-detection analyses including essential plots and statistical parameters. Group Analysis provides specialized and detailed analysis options for action potentials, decay fitting, fEPSP/population spikes, amperometry, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Synaptosoft Inc., analysis, peak, spontaneous, activity, synaptic, current, potential, spike, calcium, image, amperometric, ECG, plot, statistical, parameter | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000143, SCR_014441 | SCR_002184 | Mini Analysis, MiniAnalysis | 2026-02-15 09:18:15 | 1137 | ||||||||
|
ChIPSeq Peak Finder Resource Report Resource Website 1+ mentions |
ChIPSeq Peak Finder (RRID:SCR_002081) | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chipseq, sequencing, dna, analysis, solexa, illumina |
is listed by: OMICtools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:27863463 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00434 | https://sources.debian.org/src/chip-seq/ | SCR_002081 | ChIPSeq Toolbox | 2026-02-15 09:18:14 | 1 | ||||||
|
BrainVision Analyzer Resource Report Resource Website 100+ mentions |
BrainVision Analyzer (RRID:SCR_002356) | BVA | software application, data processing software, data analysis software, software resource | Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more. | Brain Products GmbH, neurophysiology, manage, data, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Products |
Commercially available | nlx_155717 | http://www.nitrc.org/projects/bva | SCR_002356 | BrainVision Analyzer, BrainVision Analyzer 2 | 2026-02-15 09:18:17 | 449 | ||||||
|
Image Studio Lite Resource Report Resource Website 100+ mentions |
Image Studio Lite (RRID:SCR_013715) | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software. | Li-COR, Odyssey, infrared, immunoblot, western blot, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014211 | SCR_013715 | Image Studio Lite version 3.1, LICOR Image Studio Lite Software, LI-COR Image Studio Lite Software, Image Studio Lite Software | 2026-02-15 09:20:33 | 256 | |||||||||
|
Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | software application, data processing software, data analysis software, software resource | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-02-15 09:20:50 | 2805 | ||||||||
|
Maple Resource Report Resource Website 100+ mentions |
Maple (RRID:SCR_014449) | software application, data processing software, data analysis software, software resource | Mathematical software that can compute both numeric and symbolic solutions. It can be used to analyze, explore, visualize, and solve mathematical problems. | math, analysis, mathmatics, computation, meta-analysis, numeric, symbolic | SCR_014449 | Maple Software, Maplesoft, Maple Soft, MapleSoft | 2026-02-15 09:21:03 | 148 | |||||||||||
|
FactoMineR Resource Report Resource Website 1000+ mentions |
FactoMineR (RRID:SCR_014602) | software application, data processing software, data analysis software, software resource | Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables. | multivariate, analysis, data, structure, organized, group, variable, individual, hierarchy |
is used by: ClustVis is listed by: CRAN |
https://cran.r-project.org/web/packages/FactoMineR/index.html https://github.com/husson/FactoMineR |
SCR_014602 | factominer | 2026-02-15 09:20:59 | 2349 | |||||||||
|
BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | software application, data processing software, data analysis software, software resource | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | 2026-02-15 09:21:56 | 42 | ||||||||||
|
proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | software application, data processing software, data analysis software, software resource | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-02-15 09:21:59 | 1 | |||||||
|
Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | software application, data processing software, data analysis software, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | NIH Office of the Director DP2 OD008540; NHLBI U01 HL130010; NSF PHY-1427654; NHGRI HG006193; Welch Foundation ; Cancer Prevention Research Institute of Texas ; NVIDIA Research Center Award ; IBM University Challenge Award ; Google Research Award ; McNair Medical Institute Scholar Award ; President Early Career Award in Science and Engineering ; NHGRI HG003067; PD Soros Fellowship |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-02-15 09:21:59 | 108 | ||||||||
|
ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | software application, data processing software, data analysis software, software resource | Software tools for analysis of cellular cryo-ET data. | analysis, cellular, cryo-ET, data | Free, Available for download, Freely available | SCR_017191 | 2026-02-15 09:21:16 | 5 | |||||||||||
|
BZ Analyzer software Resource Report Resource Website 10+ mentions |
BZ Analyzer software (RRID:SCR_017205) | software application, data processing software, data analysis software, software resource | Software tool as analysis application BZ-H1A by Keyence, Japan for fluorescence microscope BZ-8100 series. | analysis, BZH1A, Keyence, fluorescence, microscope | Available for purchase | SCR_017205 | 2026-02-15 09:21:59 | 13 | |||||||||||
|
TopScan Resource Report Resource Website 50+ mentions |
TopScan (RRID:SCR_017141) | software application, data processing software, data analysis software, software resource | Software suite as top view based behavior analysis system by CleverSys Inc. Uses animal body parts to provide behavior analysis results. Used in experiments with animal tracking task. | top, view, behavior, analysis, system, CleverSys Inc., animal, body, part, track, detect | SCR_017141 | TopScan Suite | 2026-02-15 09:21:58 | 94 | |||||||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | software application, data processing software, data analysis software, software resource | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-02-15 09:22:00 | 2 | ||||||
|
Cell Ranger Resource Report Resource Website 500+ mentions |
Cell Ranger (RRID:SCR_017344) | software application, data processing software, data analysis software, software resource | Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics. | Analysis, process, chromium, singe, cell, RNA-seq, align, read, barcode, matrice, clustering, gene, expression, 10xGenomics |
is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology works with: Loupe Browser |
Restricted | SCR_017344 | 2026-02-15 09:22:03 | 611 | ||||||||||
|
trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | software application, data processing software, data analysis software, software resource | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/ https://bio.tools/trimal |
SCR_017334 | 2026-02-15 09:21:19 | 582 | ||||||
|
GCE Resource Report Resource Website 10+ mentions |
GCE (RRID:SCR_017332) | software application, data processing software, data analysis software, software resource | Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics. | estimation, genomic, characteristic, analysis, k-mer, frequencey, de novo | ftp://ftp.genomics.org.cn/pub/gce | SCR_017332 | Genomic Characteristics Estimation | 2026-02-15 09:22:03 | 14 | ||||||||||
|
MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | software application, data processing software, data analysis software, software resource | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-02-15 09:22:00 | 19 | |||||||||
|
IKAP Resource Report Resource Website 1+ mentions |
IKAP (RRID:SCR_017417) | software application, data processing software, data analysis software, software resource | Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation. | Identify, cell, population, group, single, cell, RNAseq, analysis, clustering, dataset | DOI:10.1101/596817 | Free, Available for download, Freely available | SCR_017417 | Identifying K mAjor cell Population | 2026-02-15 09:22:04 | 2 |
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