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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RLMM Resource Report Resource Website 1+ mentions |
RLMM (RRID:SCR_012984) | RLMM | software resource | A Genotype Calling Algorithm for Affymetrix SNP Arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00732 | SCR_012984 | 2026-09-05 06:27:30 | 5 | ||||||||||
|
charm Resource Report Resource Website 50+ mentions |
charm (RRID:SCR_012992) | charm | software resource | Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:charm, OMICS_00792 | https://bio.tools/charm | SCR_012992 | 2026-09-05 06:27:30 | 68 | ||||||||
|
BiSeq Resource Report Resource Website 10+ mentions |
BiSeq (RRID:SCR_012993) | BiSeq | software resource | Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00620 | SCR_012993 | 2026-09-05 06:27:30 | 30 | ||||||||||
|
MEDME Resource Report Resource Website 10+ mentions |
MEDME (RRID:SCR_012995) | MEDME | software resource | Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00614 | SCR_012995 | 2026-09-05 06:27:30 | 18 | ||||||||||
|
Rolexa Resource Report Resource Website 1+ mentions |
Rolexa (RRID:SCR_013017) | Rolexa | software resource | Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01156 | SCR_013017 | 2026-09-05 06:27:31 | 1 | ||||||||||
|
cn.mops Resource Report Resource Website 10+ mentions |
cn.mops (RRID:SCR_013036) | cn.mops | software resource | A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:cn.mops, OMICS_00335 | https://bio.tools/cn.mops | SCR_013036 | Copy Number estimation by a Mixture Of PoissonS | 2026-09-05 06:27:31 | 10 | |||||||
|
HiTC Resource Report Resource Website 50+ mentions |
HiTC (RRID:SCR_013175) | HiTC | software resource | Software package to explore high-throughput ''C'' data such as 5C or Hi-C. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00524 | SCR_013175 | 2026-09-05 06:27:33 | 87 | ||||||||||
|
Repitools Resource Report Resource Website 10+ mentions |
Repitools (RRID:SCR_013242) | Repitools | software resource | Software tools for the analysis of enrichment-based epigenomic data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00619 | SCR_013242 | 2026-09-05 06:27:34 | 22 | ||||||||||
|
CancerMutationAnalysis Resource Report Resource Website |
CancerMutationAnalysis (RRID:SCR_013181) | CancerMutationAnalysis | software resource | Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer. |
is listed by: OMICtools has parent organization: Bioconductor |
Cancer | OMICS_00141 | SCR_013181 | 2026-09-05 06:27:33 | 0 | |||||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data processing software, data visualization software, software application, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-09-05 06:28:38 | 61 | ||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-09-05 06:28:40 | 0 | |||||
|
scTHI Resource Report Resource Website 1+ mentions |
scTHI (RRID:SCR_018918) | scTHI | data analysis software, data processing software, software application, software resource | Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment. | Ligand receptor, active pair, active pair ligand receptor, single cell, tumor interaction, tumor microenvironment, cells clasification | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018918 | 2026-09-05 06:28:44 | 1 | |||||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data analysis software, data analytics software, data processing software, software application, software resource | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
Icahn School of Medicine at Mount Sinai ; NHLBI U01 HL107388 |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-09-05 06:28:47 | 62 | ||||||
|
MSstats Resource Report Resource Website 100+ mentions |
MSstats (RRID:SCR_014353) | data analysis software, data processing software, software application, software resource | A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations. | data independent acquisition, statistical relative quantification, protein, peptide, data analysis software, data processing, data visualization, proteomics |
uses: R Project for Statistical Computing is used by: Skyline is listed by: Bioconductor |
National Science Foundation CAREER award 1054826 | DOI:10.1186/1471-2105-13-S16-S6 | Acknowledgement requested, Available for download | http://www.bioconductor.org/packages/release/bioc/html/MSstats.html | SCR_014353 | MSStats | 2026-09-05 06:27:46 | 239 | ||||||
|
CATALYST Resource Report Resource Website 100+ mentions |
CATALYST (RRID:SCR_017127) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation. | preprocessing, cytometry, data, normalization, bead, standard, single, cell, deconvulsion, compensation, bio.tools |
uses: CATALYSTLite is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
European Research Council ; NIDDK UC4 DK108132; PhosphonetPPM and MetastasiX SystemsX grant ; Roche Postdoctoral Fellowship ; SNSF Assistant Professorship grant ; Swiss National Science Foundation |
PMID:29605184 | Free, Available for download, Freely available | biotools:catalyst | https://github.com/HelenaLC/CATALYST, https://bio.tools/catalyst | SCR_017127 | Cytometry dATa anALYSis Tools | 2026-09-05 06:28:19 | 241 | |||||
|
GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data analysis software, data processing software, software application, 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 | 2026-09-05 06:28:18 | 53 | |||||||||
|
affydata Resource Report Resource Website |
affydata (RRID:SCR_016976) | AffyData | data analysis software, data or information resource, data processing software, software application, software resource | Software R package for analysis of Affymetrix Data. Contains samples data files of a large size. | analysis, Affymetrix, data, large, dataset, oligonucleotide, array |
is listed by: Bioconductor is related to: affy is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016976 | affydata, Affymetrix Data, Affymetrix Data for Demonstration Purpose | 2026-09-05 06:28:16 | 0 | ||||||||
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, software resource, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Edelman-Gardner Foundation ; NCI CA009363; NCI CA138249; NHGRI HG006853 |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-09-05 06:32:25 | 1 | |||||
|
Scmap Resource Report Resource Website 10+ mentions |
Scmap (RRID:SCR_017338) | data processing software, software application, software resource | Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments. | Unsupervised, projection, single, cell, RNA-seq, data |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:29608555 | Free, Available for download, Freely available | http://bioconductor.org/packages/scmap/, https://www.sanger.ac.uk/science/tools/scmap | SCR_017338 | 2026-09-05 06:30:53 | 17 | ||||||||
|
HTqPCR Resource Report Resource Website 50+ mentions |
HTqPCR (RRID:SCR_003375) | HTqPCR | data processing software, software application, software resource | Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). | data import, differential expression, gene expression, microtitre plate assay, multiple comparison, preprocessing, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19808880 | Free, Available for download, Freely available | biotools:htqpcr, OMICS_02314 | https://bio.tools/htqpcr | SCR_003375 | HTqPCR - Automated analysis of high-throughput qPCR data | 2026-09-05 06:30:39 | 74 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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