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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CuGenDB Resource Report Resource Website 100+ mentions |
CuGenDB (RRID:SCR_018401) | CuGenDB | data or information resource, topical portal, portal, database | Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops. | Genomic data, genetic data, cucurbit, data distribution, data analysis, data mining, data integration, dataset, comparative genomics, functional genomics, cucurbit crop, FASEB list | USDA National Institute of Food and Agriculture Specialty Crop Research Initiative ; US-Israel Binational Agricultural Research and Development Fund ; USDA Agricultural Research Service ; International Cucurbit Genomics Initiative |
PMID:30321383 | Free, Freely available | SCR_018401 | Cucurbit Genomics Database, Cucurbitaceae family Genomics Database | 2026-08-10 09:36:25 | 285 | |||||||
|
Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data analysis software, software application, software toolkit, software resource, data processing software | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-08-10 09:36:27 | 342 | ||||||
|
MicroFilePlus Resource Report Resource Website 1+ mentions |
MicroFilePlus (RRID:SCR_018724) | software application, data processing software, image processing software, software resource | Software tool as microscopy image file format converter by MBF Bioscience. Converts common microscopy image files to JPEG2000 and OME-TIFF. Used to view, analyze, and share big image data from many sources. | Image file format, image converter, converter, OME-TIFF Format, jpeg2000, jpx, JP2, MBF Bioscience | Restricted | SCR_018724 | MicroFilePlus, MicroFile+, microfileplus | 2026-08-10 09:36:21 | 2 | ||||||||||
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trend Resource Report Resource Website 1+ mentions |
trend (RRID:SCR_018658) | data analysis software, software application, software toolkit, software resource, data processing software | Software package includes tests for trends and change points detection. Used in analysis of environmental data. | tests for trend detection, environmental data analysis, Cox-Stuart Trend Test, Mann-Kendall Trend Test, Hirsch-Slack Test, partial Pearson and Spearman correlation trend test, change-point detection | is related to: CRAN | Free, Freely available | SCR_018658 | Non-Parametric Trend Tests and Change-Point Detection | 2026-08-10 09:36:18 | 1 | |||||||||
|
QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | data analysis software, software application, software toolkit, software resource, data processing software | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-08-10 09:36:20 | 27 | ||||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data analysis software, software application, software toolkit, software resource, data processing software | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-08-10 09:36:18 | 21 | |||||||
|
AsPredicted Resource Report Resource Website 100+ mentions |
AsPredicted (RRID:SCR_018789) | data or information resource, topical portal, portal | Website for study pre-registration. Defines minimum required criteria for pre-registration and allows authors to pre-register their study. It is standardized pre-registration that requires only what is necessary to separate exploratory from confirmatory analyses. | Study pre-registration, publish paper, evaluation, minimum required criteria, author study pre-registration, standardized pre-registration | has parent organization: University of Pennsylvania; Philadelphia; USA | Restricted | SCR_018789 | 2026-08-10 09:36:27 | 165 | ||||||||||
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Discrete Morse Resource Report Resource Website |
Discrete Morse (RRID:SCR_018662) | DM | software application, data processing software, image processing software, software resource | Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. | Neuron tracing, tracer injection, single neuron data set, set of trees summarization generation, neuron image data, extract individual neuron tree skeleton, volumetric brain image data, summarize collection, tracer injection labelled neuron | DOI:10.1101/2020.03.21.000323v1 | Free, Freely available | SCR_018662 | DiscreteMorse | 2026-08-10 09:36:20 | 0 | ||||||||
|
ABCD-ReproNim Course Resource Report Resource Website |
ABCD-ReproNim Course (RRID:SCR_018911) | data or information resource, training resource, portal, knowledge environment resource | Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes. | Adolescent Brain Cognitive Development Study data analysis, reproducible analysis, ABCD study data analysis, reprReproNim workflow instruction |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ReproNim: A Center for Reproducible Neuroimaging Computation |
Free, Freely available | SCR_018911 | Adolescent Brain Cognitive Development ReproNim Course | 2026-08-10 09:36:25 | 0 | |||||||||
|
Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | data analysis software, software application, software toolkit, software resource, data processing software | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-08-10 09:36:27 | 0 | |||||||
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Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data analysis software, software application, software toolkit, software resource, data processing software | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-08-10 09:36:27 | 9 | |||||||
|
Nurses Health Study Resource Report Resource Website 1+ mentions |
Nurses Health Study (RRID:SCR_019144) | data or information resource, topical portal, portal | Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants. | Health Data and Tools | NHS | Free, Freely available | SCR_019144 | Nurses study | 2026-08-10 09:36:31 | 6 | |||||||||
|
CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data analysis software, software application, software toolkit, software resource, data processing software | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-08-10 09:36:29 | 22 | |||||||||
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Long Ranger Resource Report Resource Website 10+ mentions |
Long Ranger (RRID:SCR_018925) | data analysis software, software application, software toolkit, software resource, data processing software | Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics. | Analysis pipelines, process chromium sequencing output, align reads, call SNPs, phase SNPs, indel, structural variant, 10x Genomics | Restricted | SCR_018925 | 2026-08-10 09:36:23 | 14 | |||||||||||
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Trinotate Resource Report Resource Website 10+ mentions |
Trinotate (RRID:SCR_018930) | data analysis software, software application, software toolkit, software resource, data processing software | Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | Automatic functional annotation, transcriptome annotation, de novo assembled transcriptome, model organism, non model organism | Free, Available for download, Freely available | SCR_018930 | Transcriptome Functional Annotation and Analysis | 2026-08-10 09:36:23 | 37 | ||||||||||
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NEMAR Resource Report Resource Website 1+ mentions |
NEMAR (RRID:SCR_019100) | data or information resource, topical portal, portal | Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource. | Human electrophysiological data, neuroelectromagnetic data, neuroelectromagnetic tools, data archives, data analysis, data visualization, EEG data, MEG data, iEEG data, ECoG data, brain data | is affiliated with: OpenNeuro | NIH | Free, Freely available | SCR_019100 | NEuroelectroMagnetic data Archive and tools Resource | 2026-08-10 09:36:27 | 9 | ||||||||
|
Engauge Digitizer Resource Report Resource Website 50+ mentions |
Engauge Digitizer (RRID:SCR_019056) | software application, data processing software, image processing software, software resource | Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves. | Image file acceptance, graph image, graph data recovery, graph conversion, data point, image file import, image digitization | Free, Available for download, Freely available | https://github.com/markummitchell/engauge-digitizer/tree/v12.2.1 | SCR_019056 | 2026-08-10 09:36:25 | 64 | ||||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | data analysis software, software application, software toolkit, software resource, data processing software | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; UCSD School of Medicine ; NIMH U19 MH114831 |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-08-10 09:36:42 | 23 | |||||||
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Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | data analysis software, software application, software toolkit, software resource, data processing software | Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data. | structural variants identification, reference genome, structural variant calls generation, whole genome sequencing data, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parliament2 | https://bio.tools/parliament2 | SCR_019187 | 2026-08-10 09:36:28 | 5 | ||||||||
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Computational Anatomy Toolbox for SPM Resource Report Resource Website 500+ mentions |
Computational Anatomy Toolbox for SPM (RRID:SCR_019184) | CAT | data analysis software, software application, software toolkit, software resource, data processing software | Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry. | MRI, neuroimaging, brain, voxel based morphometry, surface based morphometry, deformation based morphometry, label based morphometry, region based morphometry | works with: SPM | Free, Available for download, Freely available | SCR_019184 | CAT12 | 2026-08-10 09:36:31 | 581 |
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