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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
cghMCR Resource Report Resource Website 1+ mentions |
cghMCR (RRID:SCR_012898) | cghMCR | software resource | Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00710 | SCR_012898 | 2026-02-14 02:02:18 | 5 | ||||||||||
|
RankProd Resource Report Resource Website 100+ mentions |
RankProd (RRID:SCR_013046) | RankProd | software resource | Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01313 | SCR_013046 | 2026-02-14 02:02:26 | 186 | ||||||||||
|
MEDIPS Resource Report Resource Website 100+ mentions |
MEDIPS (RRID:SCR_012996) | MEDIPS | software resource | Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00613 | SCR_012996 | MeDIP-seq data analysis | 2026-02-14 02:02:25 | 168 | |||||||||
|
TurboNorm Resource Report Resource Website |
TurboNorm (RRID:SCR_012963) | TurboNorm | software resource | Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00856 | SCR_012963 | 2026-02-14 02:02:45 | 0 | ||||||||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-02-14 02:02:45 | 38 | ||||||||||
|
phyloseq Resource Report Resource Website 1000+ mentions |
phyloseq (RRID:SCR_013080) | phyloseq | software resource | Software for handling and analysis of high-throughput microbiome census data. | bio.tools |
is used by: microViz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1371/journal.pone.0061217 | OMICS_01520, biotools:phyloseq | https://bio.tools/phyloseq https://sources.debian.org/src/r-bioc-phyloseq/ |
SCR_013080 | 2026-02-14 02:02:46 | 2774 | |||||||
|
BayesPeak Resource Report Resource Website 10+ mentions |
BayesPeak (RRID:SCR_013011) | BayesPeak | software resource | Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00432 | SCR_013011 | BayesPeak - Bayesian Analysis of ChIP-seq Data | 2026-02-14 02:02:26 | 13 | |||||||||
|
ChIPseqR Resource Report Resource Website |
ChIPseqR (RRID:SCR_013016) | ChIPseqR | software resource | Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00501 | SCR_013016 | 2026-02-14 02:02:45 | 0 | ||||||||||
|
aCGH Resource Report Resource Website 100+ mentions |
aCGH (RRID:SCR_013232) | aCGH | software resource | Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00698 | SCR_013232 | 2026-02-14 02:02:23 | 135 | ||||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, software resource, data processing software, software application | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-14 02:03:30 | 2638 | ||||||
|
ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | data visualization software, data processing software, data analysis software, software application, software resource | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | Reactome Pathway Analysis | 2026-02-14 02:03:49 | 76 | ||||||
|
MSnbase Resource Report Resource Website 10+ mentions |
MSnbase (RRID:SCR_019317) | data visualization software, data processing software, data analytics software, software toolkit, software application, software resource | Software R package provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Used for isobaric tagged mass spectrometry data visualization, processing and quantitation. | Mass spectrometry data processing, mass spectrometry data visualization, raw mass spectrometry data | is listed by: Bioconductor | BBSRC Tools and Resources Development Fund ; European Union 7th Framework Program |
PMID:22113085 PMID:32902283 |
Free, Available for download, Freely available | SCR_019317 | 2026-02-14 02:03:51 | 10 | ||||||||
|
Extending Guilt by Association by Degree Resource Report Resource Website 1+ mentions |
Extending Guilt by Association by Degree (RRID:SCR_018427) | EGAD | data processing software, data analysis software, software toolkit, software application, software resource | Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks. | Extending guilt, association by degree, functional properties calculation, guilt network, association method, functional analysis, gene network | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018427 | EGAD Bioconductor, Extending guilt by association by degree | 2026-02-14 02:03:32 | 6 | ||||||||
|
StructuralVariantAnnotation Resource Report Resource Website 1+ mentions |
StructuralVariantAnnotation (RRID:SCR_018683) | data processing software, data analysis software, software toolkit, software application, software resource | Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects. | Structural variant analysis, structural variant, VCF parsing, genomic loci, GRanger object, breakpoint | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018683 | 2026-02-14 02:03:42 | 2 | ||||||||||
|
EnhancedVolcano Resource Report Resource Website 100+ mentions |
EnhancedVolcano (RRID:SCR_018931) | data visualization software, software resource, data processing software, software application | Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses. | Publication ready plot, enhanced coloring, enhanced labeling, data visualisation, differential expression analyses, plot, volcano plot |
uses: ggplot2 uses: ggrepel is listed by: Bioconductor |
Free, Available for download, Freely available | https://github.com/kevinblighe/EnhancedVolcano | SCR_018931 | 2026-02-14 02:03:27 | 469 | |||||||||
|
DEGreport Resource Report Resource Website 10+ mentions |
DEGreport (RRID:SCR_018941) | data analysis software, software resource, data processing software, software application | Software R package for creation of HTML report of differential expression analyses of count data. Integrates some of code mentioned in DESeq2 and edgeR vignettes, and reports ranked list of genes according to fold changes mean and variability for each selected gene. | HTML report creation, differential expression analyses, count data, code integration, gene list report | is listed by: Bioconductor | Free, Available for download, Freely available | http://lpantano.github.io/DEGreport | SCR_018941 | 2026-02-14 02:03:43 | 16 | |||||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, software resource, data processing software, software application | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-02-14 02:03:06 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | data processing software, alignment software, data analysis software, software application, software resource, image analysis software | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-02-14 02:03:21 | 188 | ||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, software resource, data processing software, software application | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-02-14 02:03:11 | 92 | ||||
|
Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | 2026-02-14 02:03:11 | 167 |
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