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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
seqbias Resource Report Resource Website 10+ mentions |
seqbias (RRID:SCR_006832) | seqbias | software resource | Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_01237, biotools:seqbias, BioTools:seqbias | https://bio.tools/seqbias, https://bio.tools/seqbias, https://bio.tools/seqbias | SCR_006832 | seqbias - Estimation of per-position bias in high-throughput sequencing data | 2026-07-25 12:06:29 | 30 | ||||||
|
DEGseq Resource Report Resource Website 1000+ mentions |
DEGseq (RRID:SCR_008480) | DEGseq | software resource | R package to identify differentially expressed genes from RNA-Seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01305 | SCR_008480 | 2026-07-25 12:06:48 | 1643 | ||||||||||
|
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 | 2026-07-25 12:06:16 | 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 | 2026-07-25 12:06:20 | 449 | |||||||
|
IRanges Resource Report Resource Website 50+ mentions |
IRanges (RRID:SCR_006420) | IRanges | software resource | Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible. | Annotating genomic ranges, computing genomic ranges, genomic ranges, storing ranges of integers, bio.tools |
is used by: riboWaltz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23950696 | Free, Available for download, Freely available | OMICS_01163, biotools:iranges | https://bio.tools/iranges | SCR_006420 | Infrastructure for manipulating intervals on sequences | 2026-07-25 12:06:19 | 77 | |||||
|
Fred Hutchinson Cancer Center Resource Report Resource Website 10+ mentions |
Fred Hutchinson Cancer Center (RRID:SCR_004984) | Fred Hutch Cancer Research Center | institution | Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program. | Adult cancer research and care center, UW Medicine, cancer |
is parent organization of: CODEHOP is parent organization of: Coddle-Codons Optimized to Discover Deleterious LEsions is parent organization of: Pplacer is parent organization of: International Histocompatibility Cell and DNA Bank is parent organization of: Bioconductor is parent organization of: Blocks is parent organization of: VariantAnnotation is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Proteomics Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Research Freezers and Sample Storage Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Flow Cytometry is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Specimen Processing/Research Cell Bank is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Glassware Services is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Electron Microscopy is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Experimental Histopathology Shared Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Arnold Library is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Genomics Shared Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Comparative Medicine is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Antibody Technology is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology is parent organization of: Fred Hutchinson Cancer Center Therapeutic Products Core Facility is parent organization of: Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility is parent organization of: Fred Hutchinson Cancer Center Biostatistics Shared Resource is parent organization of: Fred Hutchinson Cancer Center Collaborative Data Services Core Facility is parent organization of: Fred Hutchinson Cancer Center Genomics and Bioinformatics Core Facility is parent organization of: Fred Hutchinson Cancer Center Antibody Technology Core Facility is parent organization of: Fred Hutchinson Cancer Center Cellular Imaging Core Facility is parent organization of: Fred Hutchinson Cancer Center Comparative Medicine Core Facility is parent organization of: Fred Hutchinson Cancer Center Electron Microscopy Core Facility is parent organization of: Fred Hutchinson Cancer Center Experimental Histopathology Core Facility is parent organization of: Fred Hutchinson Cancer Center Flow Cytometry Core Facility is parent organization of: Fred Hutchinson Cancer Center Immune Monitoring Core Facility is parent organization of: Fred Hutchinson Cancer Center Preclinical Imaging Core Facility is parent organization of: Fred Hutchinson Cancer Center Preclinical Modeling Core Facility is parent organization of: Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility is parent organization of: Fred Hutchinson Cancer Center Leica Center of Excellence Core Facility is parent organization of: Fred Hutch Cancer Center Translational Pathology Core Facility |
Wikidata Q1452369, , Crossref Funder ID 100005895, ISNI 0000 0001 2180 1622, nlx_94018, GRID grid.270240.3 | https://ror.org/007ps6h72, https://www.fhcc.org/?_gl=1%2A1ewelpw%2A_ga%2AMTY0NDY4MTI0LjE2NTg5NDc1OTQ.%2A_ga_CMZTF4L2MS%2AMTY1ODk0NzU5NC4xLjEuMTY1ODk0ODUyNy4w | SCR_004984 | 2026-07-25 12:10:45 | 10 | ||||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-07-25 12:10:24 | 0 | ||||||
|
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 | rqubic - Qualitative biclustering algorithm for expression data analysis in R | 2026-07-25 12:07:42 | 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 | Differential Binding Analysis of ChIP-Seq peak data | 2026-07-25 12:07:43 | 1254 | |||||||
|
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 | Iterative Binary Biclustering of Genesets | 2026-07-25 12:07:42 | 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 | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-07-25 12:07:38 | 2 | ||||||
|
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 | 2026-07-25 12:07:41 | 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 | 2026-07-25 12:07:42 | 32 | ||||||||||
|
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 | 2026-07-25 12:07:39 | 41 | |||||||
|
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 | 2026-07-25 12:07:40 | 734 | ||||||||
|
CSAR Resource Report Resource Website 10+ 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 | 2026-07-25 12:07:41 | 49 | ||||||
|
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 | 2026-07-25 12:07:39 | 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 | 2026-07-25 12:07:39 | 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 | 2026-07-25 12:07:43 | 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 | 2026-07-25 12:07:45 | 168 |
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