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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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RnaSeqGeneEdgeRQL Resource Report Resource Website |
RnaSeqGeneEdgeRQL (RRID:SCR_016699) | data processing software, data analysis software, software toolkit, software application, software resource | Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment. | study, analysis, RNA, sequencing, read, alignment, data | is affiliated with: Bioconductor | Free, Available for download, Freely available | SCR_016699 | 2026-02-14 02:03:08 | 0 | ||||||||||
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Imaging WorkBench Resource Report Resource Website 1+ mentions |
Imaging WorkBench (RRID:SCR_016589) | IW | data processing software, data acquisition software, image acquisition software, software application, software resource, image analysis software | Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems. | multichannel, fluorescence, image, acquisition, analysis | Commercially available | SCR_016589 | IW 6, Imaging Workbench 6.0, Imaging Workbench (IW) 6, IW 6.0, Imaging Workbench 6 | 2026-02-14 02:03:17 | 4 | |||||||||
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Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | disease-related portal, data or information resource, portal, topical portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | ResMed Foundation ; Philips Respironics ; NHLBI U34 HL105277 |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-02-14 02:03:17 | 2 | ||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | data visualization software, data processing software, data analysis software, software application, software resource | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-02-14 02:03:18 | 21 | ||||||||
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NZYTech Resource Report Resource Website 10+ mentions |
NZYTech (RRID:SCR_016772) | organization | Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins. | biomaterial, analysis, service, production, supplier, molecular, biology, diagnostics, enzyme, protein | grid.436825.e, Wikidata: Q30291029 | https://ror.org/00rtryt44 | SCR_016772 | Lda. � Genes and Enzymes, NZYTech | 2026-02-14 02:03:09 | 11 | |||||||||
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smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | data analysis software, software resource, data processing software, software application | Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. | nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence | requires: SAMTOOLS | Free, Available for download, Freely available | SCR_016892 | single molecule Molecular Inversion Probesfil, smMIPfil | 2026-02-14 02:03:18 | 2 | |||||||||
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Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | data processing software, data analysis software, software toolkit, software application, software resource | Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging. | automated, processing, analysis, visualization, data, acquired, single, molecule, localization, microscopy, SMLM, imaging, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: ImageJ |
Czech Science Foundation ; Charles University ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-02-14 02:03:18 | 42 | |||||
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CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Basic Research Program of China ; Program for New Century Excellent Talents in University ; Fundamental Research Funds for the Central Universities |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-02-14 02:03:06 | 30 | |||||
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ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, software resource, data processing software, software application | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat https://www.crick.ac.uk/research/labs/peter-van-loo/software https://bio.tools/ascat https://sources.debian.org/src/r-other-ascat/ |
SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-02-14 02:03:06 | 33 | |||||
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Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data analysis software, software resource, data processing software, software application | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-02-14 02:03:20 | 42 | ||||||||
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Metab Resource Report Resource Website 1+ mentions |
Metab (RRID:SCR_016877) | Metab | data processing software, data analysis software, software toolkit, software application, software resource | Software package as a metabolomic data processing pipeline in R codes. | metabolomic, data, processing, pipeline, analysis, datasets | Health Research Council of New Zealand | DOI:10.1093/bioinformatics | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/Metab.html | SCR_016877 | Metabolome, Metab 1.0 | 2026-02-14 02:03:10 | 1 | ||||||
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OpenBMI Resource Report Resource Website 1+ mentions |
OpenBMI (RRID:SCR_016876) | data visualization software, data processing software, data analysis software, software toolkit, software application, software resource | Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time. | brain, computer, interface, analysis, signal, acquire, filter, process, visualize, data | has parent organization: Korea University; Seoul; South Korea | Free, Available for download, Freely available | http://openbmi.org/ | SCR_016876 | 2026-02-14 02:03:17 | 5 | |||||||||
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BioNano Irys system Resource Report Resource Website 10+ mentions |
BioNano Irys system (RRID:SCR_016754) | instrument resource | System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies. | instrument, Irys, system, BioNano Genomics, BioNanomatrix, optical, next, generation, mapping, sequence, assembly, structural, variation, analysis, data, | Commercially available | https://bionanogenomics.com/wp-content/uploads/2017/01/2016-Irys-System-Brochure.pdf | https://bionanogenomics.com/technology/genome-assembly/ | SCR_016754 | 2026-02-14 02:03:19 | 35 | |||||||||
|
Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | data analysis software, software resource, data processing software, software application | Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. | high, dimention, single, cell, data, phenotype, analysis, heterogeneity |
uses: Python Programming Language is related to: Rphenograph |
NIGMS R00 GM104148; NICHD DP1 HD084071; NCI R01 CA164729; NCI U54 CA121852; NCI R01 CA130826; NCI U54 CA143907; US Department of Health and Human Services HHSN272200700038C; NIH N01 HV00242; NCI P01 CA034233; NIAID U19 AI057229; NCI U54 CA149145; US FDA HHSF223201210194C; US DOD W81XWH1210591; Entertainment Industry Foundation ; Rachford and Carlota Harris Endowed Professorship ; CIRM DR1 01477; CIRM RB201592; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; Packard Fellowship for Science and Engineering ; NIH Office of the Director DP2 OD002414 |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-02-14 02:03:21 | 213 | |||||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data visualization software, data processing software, data analysis software, software application, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
National 973 Projects of China ; 2007 Chang-Jiang Scholars Program ; National Natural Science Foundation of China ; Guangdong Natural Science Research Grant ; Fundamental Research Funds for the Central Universities |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler https://guangchuangyu.github.io/software/clusterProfiler/ https://bio.tools/clusterprofiler |
SCR_016884 | Cluster Profiler | 2026-02-14 02:03:20 | 10762 | |||||
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Signal Resource Report Resource Website 10+ mentions |
Signal (RRID:SCR_017081) | data processing software, data acquisition software, data analysis software, software application, software resource | Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS. | sweep, based, data, acquisition, analysis, time, based, waveform, data, CED, transient, capture, patch, voltage, clamp, LTP study, evoked, response | Available for purchase | SCR_017081 | Signal Version 6, CED Signal, Cambridge Electronic Design Signal | 2026-02-14 02:03:23 | 13 | ||||||||||
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rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | data analysis software, software resource, data processing software, software application | Software package for reproducible classification analysis of single cell sequencing data. | reproducibility, classification, analysis, single, cell, sequencing, data, bio.tools |
is used by: Stardust is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
PMID:24204232 | Free, Available for download, Freely available | biotools:rCASC | https://kendomaniac.github.io/rCASC/ https://bio.tools/rCASC |
SCR_017005 | rCASC, reproducible Cluster Analysis of Single Cells | 2026-02-14 02:03:12 | 1 | ||||||
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Scikit-Criteria Resource Report Resource Website |
Scikit-Criteria (RRID:SCR_017084) | software resource, software library, software toolkit | Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack. | collection, multiple, criteria, decision, analysis, method, integrated, stack | is related to: Python Programming Language | Free, Available for download, Freely available | https://github.com/leliel12/scikit-criteria/blob/master/doc/source/index.rst https://github.com/leliel12/scikit-criteria |
SCR_017084 | 2026-02-14 02:03:20 | 0 | |||||||||
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Haystack Resource Report Resource Website 1+ mentions |
Haystack (RRID:SCR_017087) | data processing software, data analysis software, software toolkit, software application, software resource | Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline. | epigenetic, variability, cell, plasticity, chromatin, transcription, factor, motif, structure, gene, regulation, analysis |
is related to: Python Programming Language has parent organization: Harvard University; Cambridge; Massachusetts |
Free, Available for download, Freely available | https://github.com/pinellolab/haystack_bio | SCR_017087 | haystack, haystack_bio | 2026-02-14 02:03:23 | 3 | ||||||||
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Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | data processing software, analysis service resource, data analysis software, production service resource, service resource, software toolkit, software application, software resource | Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. | Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data | Free, Available for download, Freely available | OMICS_00850 | https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ | http://www.omicsoft.com/array-studio.php | SCR_010970 | 2026-02-14 02:02:08 | 5 |
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