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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
eisa Resource Report Resource Website 1+ mentions |
eisa (RRID:SCR_012883) | eisa | software resource | A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free | OMICS_01801, biotools:eisa | https://bio.tools/eisa | SCR_012883 | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-09-05 06:27:29 | 2 | ||||||
|
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 | 2026-09-05 06:27:30 | 0 | ||||||||||
|
Methylumi Resource Report Resource Website 10+ mentions |
Methylumi (RRID:SCR_012831) | Methylumi | software resource | Software package that provides classes for holding and manipulating Illumina methylation data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00798 | SCR_012831 | 2026-09-05 06:27:28 | 23 | ||||||||||
|
iChip Resource Report Resource Website 10+ mentions |
iChip (RRID:SCR_012958) | iChip | software resource | Software package that uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00807 | SCR_012958 | 2026-09-05 06:27:30 | 33 | ||||||||||
|
NarrowPeaks Resource Report Resource Website 10+ mentions |
NarrowPeaks (RRID:SCR_012924) | NarrowPeaks | software resource | Software package for post-processing of peaks and differential binding in ChIP-seq based on standard wiggle visualization files. The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process data in wiggle track format (WIG) commonly produced by ChIP-seq peak finders by applying FPCA over a set of selected candidate enriched regions. This is done in order to shorten the genomic locations accounting for a given proportion of variation among the enrichment-score profiles. The function ''narrowpeaks'' allows the user to discriminate between binding regions in close proximity to each other and to narrow down the length of the putative transcription factor binding sites while preserving the information present in the variability of the dataset and capturing major sources of variation. (2) Analyze differential variation when multiple ChIP-seq samples need to compared. The function ''narrowpeaksDiff'' quantifies differences between the tag-enrichment, and uses non-parametric tests on the FPC scores for testing differences between conditions. | functional principal component analysis |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License | OMICS_00449 | SCR_012924 | NarrowPeaks: Analysis of Variation in ChIP-seq using Functional PCA Statistics | 2026-09-05 06:27:29 | 49 | |||||||
|
ChAMP Resource Report Resource Website 500+ mentions |
ChAMP (RRID:SCR_012891) | ChAMP | software resource | Software package that includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations. |
is listed by: OMICtools has parent organization: Bioconductor |
Free | OMICS_01796 | SCR_012891 | ChAMP - Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 | 2026-09-05 06:27:29 | 791 | ||||||||
|
CSAR Resource Report Resource Website 50+ mentions |
CSAR (RRID:SCR_012930) | CSAR | software resource | Statistical tools for the analysis of ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21554688 | Free | OMICS_00435, biotools:csar | https://bio.tools/csar | SCR_012930 | 2026-09-05 06:27:29 | 50 | ||||||
|
CSSP Resource Report Resource Website 10+ mentions |
CSSP (RRID:SCR_012932) | CSSP | software resource | Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23665773 | Free | OMICS_00426 | SCR_012932 | ChIP-SEQ Statistical Power | 2026-09-05 06:27:29 | 16 | |||||||
|
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 | 2026-09-05 06:27:29 | 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 | 2026-09-05 06:27:31 | 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 | 2026-09-05 06:27:30 | 175 | |||||||||
|
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 | 2026-09-05 06:27:30 | 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 | 2026-09-05 06:27:32 | 3080 | |||||||
|
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 | 2026-09-05 06:27:31 | 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 | 2026-09-05 06:27:31 | 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 | 2026-09-05 06:27:34 | 136 | ||||||||||
|
arrayMagic Resource Report Resource Website 1+ mentions |
arrayMagic (RRID:SCR_010933) | arrayMagic | software resource | Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data |
is listed by: OMICtools has parent organization: Bioconductor |
BSD License | OMICS_00743 | SCR_010933 | arrayMagic - two-colour cDNA array quality control and preprocessing | 2026-09-05 06:26:50 | 1 | ||||||||
|
easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-09-05 06:27:18 | 30 | |||||
|
h5vc Resource Report Resource Website 1+ mentions |
h5vc (RRID:SCR_006039) | h5vc | software resource | Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files. | next-generation sequencing, 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:24451629 | GNU General Public License, v3 or newer | biotools:h5vc, OMICS_02243 | http://www.ebi.ac.uk/~pyl/h5vc/, https://bio.tools/h5vc | SCR_006039 | h5vc - Scalable nucleotide tallies with HDF5, h5vc - Managing alignment tallies using a hdf5 backend | 2026-09-05 06:25:46 | 2 | |||||
|
RUVSeq Resource Report Resource Website 100+ mentions |
RUVSeq (RRID:SCR_006263) | software resource | Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. | software package, unix/linux, mac os x, windows, r, differential expression, preprocessing, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25150836 | Artistic License, v2 | OMICS_05652 | SCR_006263 | RUVSeq: Remove Unwanted Variation from RNA-Seq Data | 2026-09-05 06:25:49 | 481 |
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