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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EnrichedHeatmap Resource Report Resource Website 50+ mentions |
EnrichedHeatmap (RRID:SCR_023082) | software toolkit, software resource | Software R package for comprehensive visualization of genomic signal associations. Visualizes enrichment of genomic signals on specific target regions. Used to visualize e.g. how histone marks are enriched to specific sites. | visualization of genomic signal associations, enrichment of genomic signals, specific target regions, | German Cancer Research Center-Heidelberg Center for Personalized Oncology | PMID:29618320 | Free, Available for download, Freely available | https://bioconductor.org/packages/EnrichedHeatmap/ | SCR_023082 | 2026-08-09 09:08:12 | 78 | ||||||||
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SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software toolkit, software resource | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950; NCI U24CA143835; American Cancer Society Research Scholar Grant |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SYstems Genetic Network AnaLysis | 2026-08-09 09:08:30 | 1 | ||||||||
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Algorithms and Framework for Nonnegative Matrix Factorization Resource Report Resource Website 10+ mentions |
Algorithms and Framework for Nonnegative Matrix Factorization (RRID:SCR_023124) | NMF | software toolkit, software resource | Software R package for nonnegative matrix factorization. Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. | Non-negative Matrix Factorization, nonnegative matrix factorization, |
is listed by: CRAN is related to: NMF Toolbox |
South-African National Bioinformatics Network ; Science Foundation Ireland |
DOI:10.1186/1471-2105-11-367 | Free, Available for download, Freely available | SCR_023124 | Non-negative Matrix Factorization | 2026-08-09 09:08:13 | 13 | ||||||
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Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software toolkit, software resource | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | NIMH 1RF1MH121868; The BRAIN Initiative ; Gordon and Betty Moore Foundation ; Alfred P. Sloan Foundation ; NIBIB R01EB027585; NSF 1551330 |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-08-09 09:08:36 | 12 | ||||||||
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SigProfilerMatrixGenerator Resource Report Resource Website 10+ mentions |
SigProfilerMatrixGenerator (RRID:SCR_023122) | software application, software resource | Software tool to create mutational matrices for all types of somatic mutations. Used to generate mutational matrices for set of samples with associated mutational catalogues. Used for optimized exploration and visualization of mutational patterns for all types of small mutational events. In addition to extending classification of single base substitutions, provides support for classifying doublet base substitutions and small insertions and deletions. | mutational patterns, small mutational events, create mutational matrices, somatic mutations, samples with associated mutational catalogues, | is related to: SigProfilerExtractor | Cancer Research UK Grand Challenge Award ; Singapore Ministry of Health ; Singapore National Medical Research Council |
PMID:31470794 | Free, Available for download, Freely available | https://osf.io/s93d5/wiki/home | SCR_023122 | 2026-08-09 09:08:31 | 35 | |||||||
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Regression Modeling Strategies Resource Report Resource Website 10+ mentions |
Regression Modeling Strategies (RRID:SCR_023242) | rms | software toolkit, software resource | Software R package as collection of functions that assist with streamline modeling. Works with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression. | streamline modeling, regression models, regression, generalized linear models | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/harrelfe/rms, https://cran.r-project.org/web/packages/rms/rms.pdf | SCR_023242 | 2026-08-09 09:08:33 | 41 | ||||||||
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MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software toolkit, software resource | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NSF DEB-2028280; NIAID U19AI110820; NHGRI R01HG005220; NIDDK R24DK110499; NIDDK U54DK102557 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-08-09 09:08:34 | 212 | ||||||||
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FFTrees Resource Report Resource Website |
FFTrees (RRID:SCR_023359) | software toolkit, software resource | Software package as decision algorithms for solving binary classification problems. Faster and more frugal because every node allows making decision. Apart from being faster and requiring less information, FFTs tend to be robust against overfitting, and are easy to interpret, use, and communicate. | decision algorithm, solving binary classification problems, binary classification, | is listed by: CRAN | DOI:10.1017/S1930297500006239 | Free, Available for download, Freely available | https://CRAN.R-project.org/package=FFTrees | SCR_023359 | Fast-and-Frugal Trees | 2026-08-09 09:08:35 | 0 | |||||||
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ReMM score Resource Report Resource Website 1+ mentions |
ReMM score (RRID:SCR_023095) | ReMM score | software application, software resource | Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases. | positions in human genome scoring, regulatory probability, relevance prediction, non-coding variations, SNVs and small InDels, Mendelian diseases, human genome | DOI:10.1101/2022.03.14.484240 | Free, Available for download, Freely available | https://charite.github.io/software-remm-score.html, https://search.datacite.org/works/10.5281/zenodo.1197579 | SCR_023095 | Regulatory Mendelian Mutation score | 2026-08-09 09:08:30 | 6 | |||||||
|
EnTAP Resource Report Resource Website 10+ mentions |
EnTAP (RRID:SCR_023010) | software toolkit, software resource | Software package as eukaryotic non model annotation pipeline.Used for bringing functional annotation to non-model eukaryotic transcriptomes to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. Addresses fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein-coding transcripts. | functional annotation, non model eukaryotic transcriptomes, functional gene annotation, de novo assembled transcriptomes, non-model eukaryotes, protein-coding transcripts, | has parent organization: University of Connecticut; Connecticut; USA | DOI:10.1111/1755-0998.13106 | Free, Available for download, Freely available | SCR_023010 | Eukaryotic Non-Model Transcriptome Annotation Pipeline | 2026-08-09 09:08:30 | 20 | ||||||||
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ATACseqQC Resource Report Resource Website 50+ mentions |
ATACseqQC (RRID:SCR_023103) | software toolkit, software resource | Software R package for post alignment quality assessment of ATAC-seq data. Package also contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. | Assays for Transposase-Accessible Chromatin, sequencing, quality control, assaying chromatin accessibility, post alignment quality assessment, ATAC-seq data, preprocess aligned ATAC-seq data, subsequent peak calling, | Department of Molecular ; Cell and Cancer Biology at UMass Medical School |
PMID:29490630 | Free, Available for download, Freely available | SCR_023103 | Assays for Transposase-Accessible Chromatin using sequencing Quality Control | 2026-08-09 09:08:31 | 60 | ||||||||
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ENCODE ATAC-seq pipeline Resource Report Resource Website 100+ mentions |
ENCODE ATAC-seq pipeline (RRID:SCR_023100) | software toolkit, software resource | Software pipeline to process ATAC-Seq data. Used for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data. | automated end-to-end quality control and processing, ATAC-seq, DNase-seq data, | Free, Available for download, Freely available | SCR_023100 | 2026-08-09 09:08:13 | 155 | |||||||||||
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10x Genomics Cellranger DNA Resource Report Resource Website 50+ mentions |
10x Genomics Cellranger DNA (RRID:SCR_023221) | software toolkit, software resource | Software analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation, and compare heterogeneity among cells. Used in processing of single cell DNA sequencing performed on 10x Chromium platform. | 10x Chromium platform, single cell DNA sequencing processing, Chromium single cell DNA sequencing, align reads, identify copy number variation, compare heterogeneity among cells, | Restricted | SCR_023221 | Cell Ranger DNA, 10x Genomics Cellranger DNA software, 10x Genomics Cellranger software | 2026-08-09 09:08:14 | 92 | ||||||||||
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vtree Resource Report Resource Website 1+ mentions |
vtree (RRID:SCR_023458) | software toolkit, software resource | Software R package for calculating and drawing variable trees. Variable trees display information about nested subsets of data frame. | Display information, nested subsets, data frame, calculating and drawing variable trees, variable trees | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/nbarrowman/vtree | SCR_023458 | variable tree | 2026-08-09 09:08:16 | 1 | ||||||||
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Toolkit for MIRA LAB Striatal Segmentation Resource Report Resource Website |
Toolkit for MIRA LAB Striatal Segmentation (RRID:SCR_023073) | software toolkit, software resource | Software MATLAB pipeline that produces CNN-based segmentations of striatal regions of brain based on structural T1w image. | CNN-based segmentations, brain striatal regions, structural T1w image | uses: MATLAB | PMID:33970510 | Free, Available for download, Freely available | https://github.com/MIRA-Lab-stack/Striatal_Segmentation | SCR_023073 | Toolkit_for_MIRA_LAB_Striatal_Segmentation | 2026-08-09 09:08:30 | 0 | |||||||
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ataqv Resource Report Resource Website 1+ mentions |
ataqv (RRID:SCR_023112) | software toolkit, software resource | Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments. | QC of ATAC-seq results, visualization of ATAC-seq results, examine aligned reads, mapping quality, | NIDDK R01 DK-117960; American Diabetes Association Pathway to Stop Diabetes ; NHGRI T32 HG00040; NIDDK T32 DK101357; University of Michigan Rackham Predoctoral Fellowship |
PMID:32213349 | Free, Available for download, Freely available | https://parkerlab.github.io/ataqv/demo/ | SCR_023112 | 2026-08-09 09:08:31 | 7 | ||||||||
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Guppy basecaller Resource Report Resource Website 10+ mentions |
Guppy basecaller (RRID:SCR_023196) | software toolkit, software resource | Software toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies sequencing platforms. Data processing toolkit that contains Oxford Nanopore Technologies basecalling algorithms, and several bioinformatic post-processing features. Provided as binaries to run on Windows, OS X and Linux platforms, as well as being integrated with MinKNOW, Oxford Nanopore device control software. | Oxford Nanopore Technologies, sequencing platform, basecalling algorithm, | Restricted | https://media.tghn.org/medialibrary/2021/10/ONT_bioinformatics_pipeline_-_basecalling_to_alignment_V1.1.pdf | SCR_023196 | 2026-08-09 09:08:13 | 26 | ||||||||||
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Oracle Crystal Ball Resource Report Resource Website 1+ mentions |
Oracle Crystal Ball (RRID:SCR_023226) | software application, software resource | Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics. | Spreadsheet based application, risk measurement and reporting, Monte Carlo simulation, time series forecasting, optimization | Restricted | SCR_023226 | 2026-08-09 09:08:14 | 4 | |||||||||||
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draw.io Resource Report Resource Website 1+ mentions |
draw.io (RRID:SCR_022939) | software application, software resource | Software tool as diagramming application that enables collaboration in real time. | diagramming, secure diagrams, collaboration in real-time | Restricted | SCR_022939 | 2026-08-09 09:08:29 | 1 | |||||||||||
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Sapporo service Resource Report Resource Website 1+ mentions |
Sapporo service (RRID:SCR_023202) | software application, software resource | Software for standard implementation conforming to Global Alliance for Genomics and Health Workflow Execution Service API specification. | GA4GH, Global Alliance for Genomics and Health, Workflow Execution Service, API specification | is related to: Sapporo web | Free, Available for download, Freely available | SCR_023202 | Sapporo-service | 2026-08-09 09:08:32 | 1 |
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