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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | software application, data processing software, data analysis software, software resource | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download https://bio.tools/binpacker |
SCR_017038 | 2026-02-15 09:21:54 | 10 | ||||||
|
cgpBattenberg Resource Report Resource Website 10+ mentions |
cgpBattenberg (RRID:SCR_017092) | software application, data processing software, data analysis software, software resource | Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data. | installation, helper, perl, wrapper, detect, subclonality, copy, number, NGS, next, generation, sequencing, data | is related to: battenberg | Free, Available for download, Freely available | SCR_017092 | 2026-02-15 09:21:58 | 11 | ||||||||||
|
3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | software application, data processing software, data analysis software, software resource | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-02-15 09:21:17 | 40 | ||||||||||
|
GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | software application, data processing software, data analysis software, software resource | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-02-15 09:21:55 | 50 | |||||||||
|
Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | software application, data processing software, data analysis software, software resource | Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments. | analysis, sequencing, data, command, line, expression, normalization, convert | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_17554 | https://github.com/csbbcompbio | SCR_017234 | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-02-15 09:21:17 | 6 | ||||||
|
PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | software application, data processing software, data analysis software, software resource | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-02-15 09:21:59 | 17 | ||||||
|
Mass spectrometry imaging workbench Resource Report Resource Website 50+ mentions |
Mass spectrometry imaging workbench (RRID:SCR_017410) | software application, data processing software, data analysis software, software resource | Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging. | Analysis, mass, spectrometry, imaging, data, Galaxy, framework, imzML, file, quality, control, visualization, statistics, docker, container | is related to: University of Freiburg; Baden-Wurttemberg; Germany | DOI:10.1101/628719 | Free, Available for download, Freely available | https://github.com/foellmelanie/docker-galaxy-msi https://galaxyproject.org/use/msi/ |
SCR_017410 | 2026-02-15 09:22:02 | 98 | ||||||||
|
CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | software application, data processing software, data analysis software, software resource | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-02-15 09:22:00 | 489 | |||||||||
|
Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | software application, data processing software, data analysis software, software resource | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-02-15 09:21:19 | 15 | |||||||||
|
fastMNN Resource Report Resource Website 1+ mentions |
fastMNN (RRID:SCR_017351) | software application, data processing software, data analysis software, software resource | Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method. | Correct, batch, effect, single, cell, expression, data, fast, version, mutual, nearest, neighbors | Free, Available for download, Freely available | SCR_017351 | Fast Mutual Nearest Neighbors | 2026-02-15 09:22:01 | 7 | ||||||||||
|
Mediation Analysis of Causality under Confounding Resource Report Resource Website |
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) | MACC | software application, data processing software, data analysis software, software resource | Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. | Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: CRAN |
NIBIB EB022911 | Free, Available for downloads, Freely available | SCR_017442 | Mediation Analysis of Causality under Confounding, macc | 2026-02-15 09:22:04 | 0 | |||||||
|
brainGraph Resource Report Resource Website 10+ mentions |
brainGraph (RRID:SCR_017260) | software application, data processing software, data analysis software, software resource | Software R package for performing graph theory analyses of brain MRI data. | graph, theory, analysis, brain, MRI, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CRAN |
Free, Available for download, Freely available | https://www.nitrc.org/projects/braingraph/ https://rdrr.io/cran/brainGraph/ https://www.r-pkg.org/pkg/brainGraph |
SCR_017260 | brainGraph - Graph Theory Analysis of Brain MRI Data in R, brainGraph | 2026-02-15 09:22:01 | 11 | ||||||||
|
CLC Genomics Server Resource Report Resource Website 10+ mentions |
CLC Genomics Server (RRID:SCR_017396) | software application, data processing software, data analysis software, software resource | Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler. | high, throughput, sequencing, analysis, data | works with: CLC Genomics Workbench | Restricted | SCR_017396 | 2026-02-15 09:22:01 | 18 | ||||||||||
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Data Information System - DAISY Resource Report Resource Website 1+ mentions |
Data Information System - DAISY (RRID:SCR_017472) | DAISY | web application, software resource | Open source web application that allows biomedical research institutions to map their data and data flows in accordance with GDPR's accountability requirement. | Map, data, flow, GDPR | Free, Available for download, Freely available | https://github.com/elixir-luxembourg/daisy | SCR_017472 | DAta Information SYstem | 2026-02-15 09:22:06 | 2 | ||||||||
|
Willoughby–Hoye Python Scripts A-D Resource Report Resource Website 1+ mentions Issue |
Willoughby–Hoye Python Scripts A-D (RRID:SCR_017562) | software application, data processing software, data analysis software, software resource | Software tool as scripts for calculating NMR chemical shifts. Warning - this group of Python scripts used to process NMR data, described in Willoughby et al, 2014, has been found to contain bug. Please see PMID:31591889. | Python, NMR, script, caluclating, chemical, shift, data | NIA R01 AG039468 | PMID:24556787 PMID:31591889 |
Free, Freely available | SCR_017562 | 2026-02-15 09:22:08 | 1 | |||||||||
|
GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | software application, data processing software, data analysis software, software resource | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-02-15 09:22:05 | 3 | |||||
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PoloPlus USB Drive software Resource Report Resource Website 10+ mentions |
PoloPlus USB Drive software (RRID:SCR_017614) | software application, data processing software, data analysis software, software resource | Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB. | LeOra Software LLC, grouped, data, analysis, USB, drive, probit, logit | Restricted | SCR_017614 | Probit Or LOgit Plus USB Drive, PoloPlus USB Drive | 2026-02-15 09:22:05 | 35 | ||||||||||
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Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | software application, data processing software, data analysis software, software resource | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-02-15 09:22:06 | 8 | |||||||||||
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fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | software application, data processing software, data analysis software, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-02-15 09:22:11 | 23 | |||||||
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SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | web application, software resource | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2026-02-15 09:22:11 | 1 |
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