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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-02-07 02:07:28 | 34 | |||||
|
FlexProt: flexible protein alignment Resource Report Resource Website 1+ mentions |
FlexProt: flexible protein alignment (RRID:SCR_007306) | software resource | FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
nif-0000-00159, biotools:flexprot | https://bio.tools/flexprot | SCR_007306 | FlexPROT | 2026-02-07 02:07:20 | 1 | ||||||||
|
Taipan Resource Report Resource Website 1+ mentions |
Taipan (RRID:SCR_007330) | Taipan | software resource | A fast hybrid short-read assembly tool. | c, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19535537 | GNU General Public License, v2 | OMICS_00035, biotools:taipan | https://bio.tools/taipan | SCR_007330 | 2026-02-07 02:07:39 | 2 | ||||||
|
EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-02-07 02:07:34 | 18 | |||||
|
RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html https://bio.tools/ramigo |
SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2026-02-07 02:07:35 | 11 | |||||
|
BarraCUDA Resource Report Resource Website 1+ mentions |
BarraCUDA (RRID:SCR_006881) | BarraCUDA | software resource | A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: SourceForge |
PMID:22244497 PMID:19451168 |
Acknowledgement requested | OMICS_00650, biotools:barracuda | https://bio.tools/barracuda | SCR_006881 | 2026-02-07 02:07:16 | 4 | ||||||
|
Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna https://bio.tools/myrna |
SCR_006951 | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-02-07 02:07:35 | 2 | |||||
|
FGDP Resource Report Resource Website |
FGDP (RRID:SCR_008910) | FGDP | software resource | A Java-based, Microarray or Genechip data analysis system. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Fox Chase Cancer Center |
PMID:14734324 | GNU General Public License | OMICS_00756, biotools:fgdp | https://bio.tools/fgdp | SCR_008910 | Functional Genomics Data Pipeline (FGDP), Functional Genomics Data Pipeline | 2026-02-07 02:07:33 | 0 | |||||
|
iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-02-07 02:07:52 | 11 | ||||||
|
SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-02-07 02:07:39 | 21 | |||||||
|
IsoEM Resource Report Resource Website 10+ mentions |
IsoEM (RRID:SCR_009993) | IsoEM | software resource | Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Connecticut; Connecticut; USA |
biotools:isoem, OMICS_01278 | https://bio.tools/isoem | SCR_009993 | 2026-02-07 02:07:55 | 10 | ||||||||
|
BitSeq Resource Report Resource Website 10+ mentions |
BitSeq (RRID:SCR_009904) | BitSeq | software resource | A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btv483 DOI:10.1093/bioinformatics/bts260 |
, OMICS_01269, biotools:bitseq | https://bio.tools/bitseq https://sources.debian.org/src/bitseq/ |
SCR_009904 | 2026-02-07 02:07:40 | 19 | |||||||
|
MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., 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 has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-02-07 02:07:50 | 462 | |||||||
|
OntoQuest Resource Report Resource Website |
OntoQuest (RRID:SCR_013281) | OntoQuest | software resource | An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework. | ontology, interoperability, owl, middleware, web service, bio.tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: NIFSTD is related to: NIF Web Services has parent organization: Neuroscience Information Framework |
PMID:18958629 | biotools:list_ontologies, biotools:ontoquest_ws, nlx_151737 | https://bio.tools/list_ontologies https://bio.tools/ontoquest_ws |
SCR_013281 | Ontoquest | 2026-02-07 02:08:48 | 0 | ||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-02-07 02:08:48 | 7 | ||||||||
|
CEM Resource Report Resource Website 1+ mentions |
CEM (RRID:SCR_013241) | CEM | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
OMICS_01271, biotools:cem | https://bio.tools/cem | SCR_013241 | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | 2026-02-07 02:08:47 | 1 | |||||||
|
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 | 2026-02-07 02:08:46 | 34 | ||||||
|
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 | 2026-02-07 02:08:49 | 69 | ||||||||
|
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 | 2026-02-07 02:08:49 | 52 | |||||||
|
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers Resource Report Resource Website 1+ mentions |
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) | PCS | software resource | A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs. | perl, perl script, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
biotools:pcs, nlx_33020 | https://bio.tools/pcs | http://bioinfo.au.tsinghua.edu.cn/member/~gujin/pcs/ | SCR_013409 | Pairwise Conservation Scores | 2026-02-07 02:08:51 | 3 |
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