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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-02-14 02:02:50 | 37 | ||||||
|
CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-02-14 02:02:28 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-02-14 02:02:22 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-02-14 02:02:28 | 66 | ||||||||||
|
HMMSplicer Resource Report Resource Website 1+ mentions |
HMMSplicer (RRID:SCR_013315) | HMMSplicer | software resource | An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
OMICS_01241 | SCR_013315 | 2026-02-14 02:02:47 | 3 | ||||||||||
|
Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-02-14 02:02:47 | 69 | ||||||||
|
NEUMA Resource Report Resource Website 1+ mentions |
NEUMA (RRID:SCR_013324) | NEUMA | software resource | Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
PMID:21059678 | OMICS_01281 | SCR_013324 | Normalization by Expected Uniquely Mappable Area | 2026-02-14 02:02:29 | 5 | ||||||||
|
chimerascan Resource Report Resource Website 50+ mentions |
chimerascan (RRID:SCR_013298) | chimerascan | software resource | Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data. | Gene fusion detection, paired-end RNA sequencing data, RNA sequencing data, chimeric transcripts detection, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:chimerascan, OMICS_01343 | https://bio.tools/chimerascan | SCR_013298 | 2026-02-14 02:02:29 | 53 | |||||||
|
wapRNA Resource Report Resource Website 1+ mentions |
wapRNA (RRID:SCR_013292) | wapRNA | software resource | A free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of Applied Biosystems (SOLiD). | is listed by: OMICtools | PMID:21896507 | OMICS_00370 | SCR_013292 | 2026-02-14 02:02:29 | 1 | |||||||||
|
RosettaDock Resource Report Resource Website 100+ mentions |
RosettaDock (RRID:SCR_013393) | RosettaDock | software resource | Predicts the structure of a protein-protein complex from the individual structures of the monomer components. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_01604 | SCR_013393 | 2026-02-14 02:02:25 | 118 | ||||||||||
|
ArrayOligoSelector Resource Report Resource Website 10+ mentions |
ArrayOligoSelector (RRID:SCR_013494) | ArrayOligoSelector | software resource | Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
PMID:12620119 | Free, Public, Commercial requires license, Use of the blat or gfclient options requires license | OMICS_00826 | SCR_013494 | 2026-02-14 02:02:30 | 13 | ||||||||
|
TreeView Resource Report Resource Website 1000+ mentions |
TreeView (RRID:SCR_013503) | TreeView | software resource | Software to graphically browse results of clustering and other analyses from Cluster. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1093/bioinformatics/bth349 | OMICS_01574 | https://sources.debian.org/src/treeview/ | SCR_013503 | 2026-02-14 02:02:52 | 2742 | ||||||||
|
ScanAlyze Resource Report Resource Website 10+ mentions |
ScanAlyze (RRID:SCR_013507) | ScanAlyze | software resource | Software to process fluorescent images of microarrays. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
OMICS_00846 | SCR_013507 | 2026-02-14 02:02:26 | 43 | ||||||||||
|
CNV-seq Resource Report Resource Website 100+ mentions |
CNV-seq (RRID:SCR_013357) | CNV-seq | software resource | A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:cnv-seq, OMICS_00339 | https://bio.tools/cnv-seq | SCR_013357 | 2026-02-14 02:02:51 | 167 | |||||||
|
MEDEA Resource Report Resource Website 100+ mentions |
MEDEA (RRID:SCR_013356) | MEDEA | software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash. |
is listed by: OMICtools has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00941 | SCR_013356 | 2026-02-14 02:02:29 | 119 | |||||||||
|
AffinDB Resource Report Resource Website |
AffinDB (RRID:SCR_001690) | AffinDB | data or information resource, database |
Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms: # Summary information for PDB entry # Affinity information window # Tabular reports |
protein-ligand complex, affinity |
is listed by: OMICtools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Philipps-University Marburg; Marburg; Germany |
PMID:16381925 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02536, OMICS_01897 | http://www.agklebe.de/affinity | SCR_001690 | Affinity Database, AffinDB - Affinity Database For Protein-Ligand Complexes | 2026-02-14 02:06:05 | 0 | |||||
|
ProTISA Resource Report Resource Website 1+ mentions |
ProTISA (RRID:SCR_002138) | ProTISA | data or information resource, database | Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq. | translation initiation site, annotation, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:17942412 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01871 | SCR_002138 | 2026-02-14 02:06:05 | 1 | |||||||
|
STIFDB Resource Report Resource Website 10+ mentions |
STIFDB (RRID:SCR_002131) | STIFDB | data or information resource, database | Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method. | stress responsive, transcription factor, biotic, abiotic, gene, transcription factor binding site, promoter, stress, chromosome, blast |
is listed by: OMICtools has parent organization: Tata Institute of Fundamental Research; Mumbai; India |
PMID:23314754 PMID:19841686 |
Free, Freely Available | OMICS_01866 | SCR_002131 | Stress Responsive Transcription Factor Database | 2026-02-14 02:05:38 | 10 | ||||||
|
pSTIING Resource Report Resource Website 1+ mentions |
pSTIING (RRID:SCR_002045) | pSTIING | data or information resource, database | A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis. | protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, gene |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University College London; London; United Kingdom |
Inflammation, Tumor, Cancer | PMID:16381926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01916 | SCR_002045 | Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway, Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway | 2026-02-14 02:05:37 | 2 | |||||
|
WebGeSTer DB Resource Report Resource Website 1+ mentions |
WebGeSTer DB (RRID:SCR_002165) | WebGeSTer DB | data or information resource, database | Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. | genome, terminator, transcription, plasmid, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20972211 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:webgester_db, OMICS_01862 | https://bio.tools/webgester_db | SCR_002165 | WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database | 2026-02-14 02:06:08 | 5 |
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