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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
sva package Resource Report Resource Website 100+ mentions |
sva package (RRID:SCR_012836) | sva package | software resource | Contains functions for removing batch effects and other unwanted variation in high-throughput experiment. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00861 | SCR_012836 | SciCrunch Registry | Surrogate Variable Analysis | 2026-11-07 11:57:52 | 100 | |||||||||
|
TargetScore Resource Report Resource Website 1+ mentions |
TargetScore (RRID:SCR_012933) | TargetScore | software resource | Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24135265 | Free | OMICS_00421 | SCR_012933 | SciCrunch Registry | TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information | 2026-11-07 11:57:39 | 3 | |||||||
|
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 | SciCrunch Registry | 2026-11-07 11:57:41 | 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 | SciCrunch Registry | 2026-11-07 11:57:34 | 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 | SciCrunch Registry | 2026-11-07 11:57:41 | 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 | SciCrunch Registry | 2026-11-07 11:57:41 | 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 | SciCrunch Registry | 2026-11-07 11:57:34 | 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 | SciCrunch Registry | Copy Number estimation by a Mixture Of PoissonS | 2026-11-07 11:57:59 | 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 | SciCrunch Registry | 2026-11-07 11:57:36 | 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 | SciCrunch Registry | 2026-11-07 11:57:45 | 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 | SciCrunch Registry | 2026-11-07 11:57:44 | 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 | SciCrunch Registry | 2026-11-07 11:59:04 | 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 | SciCrunch Registry | Mutual Information NETworks | 2026-11-07 11:58:54 | 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 | SciCrunch Registry | 2026-11-07 11:59:12 | 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 | SciCrunch Registry | 2026-11-07 11:59:17 | 62 | ||||||
|
SynergyFinder Resource Report Resource Website 500+ mentions |
SynergyFinder (RRID:SCR_019318) | data processing software, data visualization software, software application, software resource, software toolkit | Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations. | Synergy scores, drug combinations, popular synergy scoring models, dimensional interaction surface, dose matrix, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: SynergyFinder web application |
DOI:10.1007/978-1-4939-7493-1_17 | Free, Available for download, Freely available | biotools:synergyfinder | https://bio.tools/synergyfinder | SCR_019318 | SciCrunch Registry | synergyfinder | 2026-11-07 11:59:19 | 624 | ||||||
|
CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | data analysis software, data processing software, software application, software resource | Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. | Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian has parent organization: University of Sydney; Sydney; Australia |
PMID:32353146 | Free, Available for download, Freely available | biotools:citefuse | https://bioconductor.org/packages/CiteFuse/, https://github.com/SydneyBioX/CiteFuse/, http://shiny.maths.usyd.edu.au/CiteFuse/, https://bio.tools/CiteFuse | SCR_019321 | SciCrunch Registry | Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse | 2026-11-07 11:59:12 | 3 | ||||||
|
tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data analysis software, data processing software, software application, software resource | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
European Commission ; NCI T32 CA009337; SNSF 143883 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | SciCrunch Registry | tximport v1.4.0 | 2026-11-07 12:00:41 | 100 | ||||
|
MetaNeighbor Resource Report Resource Website 50+ mentions |
MetaNeighbor (RRID:SCR_016727) | data analysis software, data processing software, software application, software resource | Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting. | quantify, cell, type, replicability, dataset, access, cell, type, identity, functional, random, gene |
is used by: BICCN is listed by: Bioconductor is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/maggiecrow/MetaNeighbor, https://github.com/gillislab/MetaNeighbor | SCR_016727 | SciCrunch Registry | 2026-11-07 12:00:48 | 58 | |||||||||
|
GLAD Resource Report Resource Website 100+ mentions |
GLAD (RRID:SCR_001284) | GLAD | software resource | Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified. | comparative genomic hybridization, breakpoint, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15381628 | Free, Available for download, Freely available | OMICS_02053 | SCR_001284 | SciCrunch Registry | GLAD - Gain and Loss Analysis of DNA, Gain and Loss Analysis of DNA | 2026-11-07 12:00:54 | 292 |
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