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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||||||
|
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 | ||||||||||
|
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 | |||||||
|
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 | ||||||||
|
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 | ||||||||||
|
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 | |||||||||||
|
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 | |||||||||||
|
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 | |||||||||
|
ThermoFisher Connect Platform Resource Report Resource Website 50+ mentions |
ThermoFisher Connect Platform (RRID:SCR_023441) | software application, software resource | Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment. | ThermoFisher, integrating software, integrating instruments, integrating data, laboratory ecosystem, | Restricted | SCR_023441 | Connect Platform | 2026-08-09 09:08:36 | 55 | ||||||||||
|
Generate tools Resource Report Resource Website 1+ mentions |
Generate tools (RRID:SCR_023042) | software toolkit, software resource | Software pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. Tools for handling and analysing data with ambiquities. | HLA data analysis, handling and analysing data with ambiquities, handling and analysing data, data with ambiquities, | PMID:24738646 | Free, Available for download, Freely available | SCR_023042 | HLA-net GENE[RATE], Gene[rate] tools | 2026-08-09 09:08:29 | 1 | |||||||||
|
Anipose Resource Report Resource Website 1+ mentions |
Anipose (RRID:SCR_023041) | software toolkit, software resource | Software package for 3D pose estimation. Uses DeepLabCut for 2D tracking and uses triangulation methods to project pose estimations into three dimensions.Toolkit for robust markerless 3D pose estimation. | OpenBehavior, 3D pose estimation, project pose estimations into three dimensions, markerless 3D pose estimation |
uses: DeepLabCut is listed by: OpenBehavior is related to: DeepLabCut Project |
NINDS F31NS115477; NINDS R00 NS088193; NINDS DP2NS105555; NINDS R01NS111479; NINDS U19NS112959; Searle Scholars Program ; Pew Charitable Trusts ; McKnight Foundation ; Sloan Research Fellowship ; Washington Research Foundation ; NINDS R01NS102333; NINDS U19NS104655; New York Stem Cell Foundation |
PMID:34592148 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/?s=Anipose | SCR_023041 | 2026-08-09 09:08:11 | 4 | |||||||
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xAtlas Resource Report Resource Website 1+ mentions |
xAtlas (RRID:SCR_022987) | software application, software resource | Software tool as variant caller for SNVs and small indels. Implemented as software application written in C++ . | Single nucleotide variants, variant caller, SNVs, small indels | has parent organization: Baylor College of Medicine Human Genome Sequencing Center | Free, Available for download, Freely available | SCR_022987 | 2026-08-09 09:08:10 | 3 | ||||||||||
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Starr Life Sciences MouseOx Plus Resource Report Resource Website 10+ mentions |
Starr Life Sciences MouseOx Plus (RRID:SCR_022984) | software application, software resource | Software is part of MouseOx Plus pulse oximeter system. | Starr Life Sciences Corp., MouseOx Plus oximeter system, pulse oximeter | Free, Available to download | https://www.starrlifesciences.com/product/pulse-oximetry-software/ | SCR_022984 | MouseOx Plus, MOUSEOX PLUS 2.0 | 2026-08-09 09:08:28 | 11 | |||||||||
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Mouse Behavioral Analysis Toolbox Resource Report Resource Website 1+ mentions |
Mouse Behavioral Analysis Toolbox (RRID:SCR_023291) | MouBeAT | software toolkit, software resource | Software package to analyze different behavioral tests in rodents semi-automatically. These tests include Open Field (OF), Elevated Plus Maze (EPM), Y-maze (YM) test and Morris Water Maze (MWM). | OpenBehavior, behavioral tests, behavioral tests analysis, tests in rodents |
uses: ImageJ is listed by: OpenBehavior |
Ministry of Science and Innovation ; Spain ; European Regional Development Fund |
PMID:30245618 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/moubeat/ | SCR_023291 | 2026-08-09 09:08:35 | 1 | ||||||
|
findmaxima2d Resource Report Resource Website 1+ mentions |
findmaxima2d (RRID:SCR_023332) | software application, software resource | Software Python 2D Maxima finding algorithm. Re-implementation of Java plugin for ImageJ/Fiji. | Python, 2D Maxima finding algorithm, Java plugin | Free, Available for download, Freely available | https://github.com/dwaithe/MaximaFinder/tree/master/findmaxima2d | SCR_023332 | 2026-08-09 09:08:36 | 1 | ||||||||||
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vcfR Resource Report Resource Website 1+ mentions |
vcfR (RRID:SCR_023453) | software toolkit, software resource | Software R package to read, write, manipulate and analyze variant call format data. Facilitates easy manipulation of variant call format (VCF) data. | Manipulate and visualize VCF data, variant call format data, VCF data, extract data matrices, genomic data visualization, VCF file, variant call format files, | is listed by: CRAN | Free, Available for download, Freely available | https://knausb.github.io/vcfR_documentation/, https://github.com/knausb/vcfR, https://cran.r-project.org/web/packages/vcfR/vignettes/intro_to_vcfR.html, | SCR_023453 | variant call format in R | 2026-08-09 09:08:36 | 9 | ||||||||
|
poppr Resource Report Resource Website 10+ mentions |
poppr (RRID:SCR_023452) | software toolkit, software resource | Software R package for analysis of populations with mixed modes of sexual and clonal reproduction. Used for genetic analysis of populations with mixed reproduction. | genetic analysis, mixed reproduction, mixed reproduction populations, mixed modes, sexual and clonal reproduction, | US Department of Agriculture ; USDA National Institute of Food and Agriculture ; USDA ARS Floriculture Nursery Initiative ; USDA-Forest Service Forest Health Monitoring Program |
DOI:10.7717/peerj.281 DOI:10.3389/fgene.2015.00208 |
Free, Available for download, Freely available | https://CRAN.R-project.org/package=poppr, https://github.com/grunwaldlab/poppr/ | SCR_023452 | 2026-08-09 09:08:39 | 14 | ||||||||
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Computing Chance Corrected Agreement Coefficients Resource Report Resource Website 1+ mentions |
Computing Chance Corrected Agreement Coefficients (RRID:SCR_023176) | irrCAC | software toolkit, software resource | Software R package to calculate various chance-corrected agreement coefficients among 2 or more raters. Among CAC coefficients covered are Cohen's kappa, Conger's kappa, Fleiss' kappa, Brennan-Prediger coefficient, Gwet's AC1/AC2 coefficients, and Krippendorff's alpha. Multiple sets of weights are proposed for computing weighted analyses. | CAC coefficients, chance-corrected agreement coefficients calculations, computing weighted analyses | is listed by: CRAN | Free, Available for download, Freely available | SCR_023176 | Computing Chance-Corrected Agreement Coefficients | 2026-08-09 09:08:32 | 2 |
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