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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | data analysis software, data processing software, software application, software resource, software tool | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
European Union’s 7th Framework Programme ; International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337 |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | SciCrunch Registry | 2026-11-07 12:00:51 | 50789 | |||||||
|
GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | data analysis software, data processing software, software application, software resource, software toolkit | Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner. | Gene set enrichment, variation estimation, pathway activity, sample population, microarray, RNA-seq, data analysis | is listed by: Bioconductor | ISCIII COMBIOMED ; NCI U54 CA149237; Spanish MINECO |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | SciCrunch Registry | Gene Set Variation Analysis | 2026-11-07 12:00:20 | 333 | ||||||
|
SimFFPE Resource Report Resource Website 1+ mentions |
SimFFPE (RRID:SCR_021085) | simulation software, software application, software resource | Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls. | FFPE, NGS read simulator, artifact chimeric read, next generation sequencing process, normal reads simulation, artifact chimeric reads simulation, formalin fixed paraffin embedded tissue, |
is listed by: Bioconductor is related to: CRAN |
Free, Available for download, Freely available | SCR_021085 | SciCrunch Registry | NGS Read Simulator for FFPE Tissue, Simulator for FFPE Tissue | 2026-11-07 12:00:20 | 1 | |||||||||
|
PhenStat Resource Report Resource Website 10+ mentions |
PhenStat (RRID:SCR_021317) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
NHGRI U54 HG006370; Wellcome Trust |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | SciCrunch Registry | 2026-11-07 11:59:54 | 11 | ||||||
|
svaNUMT Resource Report Resource Website 1+ mentions |
svaNUMT (RRID:SCR_021381) | data analysis software, data processing software, software application, software resource | Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls. | Nuclear mitochondrial integration events, NUMT, NUMT detection, structural variant calls. | is listed by: Bioconductor | Free, Available for download, Freely available | https://bioconductor.org/packages/svaNUMT/ | SCR_021381 | SciCrunch Registry | 2026-11-07 12:00:18 | 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 | SciCrunch Registry | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-11-07 11:57:24 | 30 | |||||
|
CRLMM Resource Report Resource Website 10+ mentions |
CRLMM (RRID:SCR_012580) | CRLMM | software resource | Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00717 | SCR_012580 | SciCrunch Registry | 2026-11-07 11:57:29 | 10 | ||||||||||
|
LVSmiRNA Resource Report Resource Website |
LVSmiRNA (RRID:SCR_012752) | LVSmiRNA | software resource | Software for normalization of Agilent miRNA arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00784 | SCR_012752 | SciCrunch Registry | 2026-11-07 11:57:38 | 0 | ||||||||||
|
MMDiff Resource Report Resource Website 1+ mentions |
MMDiff (RRID:SCR_012692) | MMDiff | software resource | Software package that detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. |
is listed by: OMICtools has parent organization: Bioconductor |
Free | OMICS_00474 | SCR_012692 | SciCrunch Registry | MMDiff - Statistical Testing for ChIP-Seq data sets | 2026-11-07 11:57:37 | 8 | ||||||||
|
baySeq Resource Report Resource Website 100+ mentions |
baySeq (RRID:SCR_012795) | baySeq | software resource | Software package that identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20698981 | OMICS_01299 | SCR_012795 | SciCrunch Registry | 2026-11-07 11:57:36 | 121 | |||||||||
|
RPA Resource Report Resource Website 1+ mentions |
RPA (RRID:SCR_012768) | RPA | software resource | A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00778 | SCR_012768 | SciCrunch Registry | RPA: Robust Probabilistic Averaging for probe-level analysis | 2026-11-07 11:57:38 | 1 | |||||||||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | SciCrunch Registry | 2026-11-07 11:57:50 | 319 | ||||||||
|
rqubic Resource Report Resource Website |
rqubic (RRID:SCR_012869) | rqubic | software resource | This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19509312 | Free | biotools:rqubic, OMICS_01799 | https://bio.tools/rqubic | SCR_012869 | SciCrunch Registry | rqubic - Qualitative biclustering algorithm for expression data analysis in R | 2026-11-07 11:57:38 | 0 | |||||
|
DiffBind Resource Report Resource Website 1000+ mentions |
DiffBind (RRID:SCR_012918) | DiffBind | software resource | Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
biotools:diffbind, OMICS_00471 | https://bio.tools/diffbind | SCR_012918 | SciCrunch Registry | Differential Binding Analysis of ChIP-Seq peak data | 2026-11-07 11:57:33 | 1449 | |||||||
|
iBBiG Resource Report Resource Website 1+ mentions |
iBBiG (RRID:SCR_012882) | iBBiG | software resource | A bi-clustering algorithm which is optimizes for binary data analysis. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22789589 | Free | OMICS_01802 | SCR_012882 | SciCrunch Registry | Iterative Binary Biclustering of Genesets | 2026-11-07 11:57:32 | 3 | |||||||
|
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 | SciCrunch Registry | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-11-07 11:57:40 | 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 | SciCrunch Registry | 2026-11-07 11:57:40 | 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 | SciCrunch Registry | 2026-11-07 11:57:39 | 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 | SciCrunch Registry | 2026-11-07 11:57:56 | 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 | SciCrunch Registry | NarrowPeaks: Analysis of Variation in ChIP-seq using Functional PCA Statistics | 2026-11-07 11:57:33 | 49 |
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