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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
WaveCNV Resource Report Resource Website 1+ mentions |
WaveCNV (RRID:SCR_012244) | WaveCNV | software resource | Cancer specific CNV caller for Next Generation sequence. | cancer | is listed by: OMICtools | PMID:24192544 | OMICS_00353 | SCR_012244 | 2026-08-08 12:00:09 | 2 | ||||||||
|
Burrows-Wheeler transform Resource Report Resource Website 1+ mentions |
Burrows-Wheeler transform (RRID:SCR_012304) | BWT | software resource | Software tool as data transformation algorithm that restructures data in such a way that the transformed message is more compressible. Used for large scale compression of genomic sequence databases. | Large scale compression, data transformation, genomic sequence databases compression, |
is listed by: OMICtools is related to: RopeBWT2 is related to: BEETL-fastq |
PMID:22556365 | Free, Freely available | OMICS_00950 | SCR_012304 | Burrows-Wheeler Transform | 2026-08-08 11:59:58 | 8 | ||||||
|
npstat Resource Report Resource Website 1+ mentions |
npstat (RRID:SCR_012128) | software resource | Software that implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:24102736 | OMICS_05826 | SCR_012128 | 2026-08-08 11:59:58 | 3 | |||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | Network Analysis and Inference Library | 2026-08-08 11:59:40 | 8 | ||||||
|
iMSAT Resource Report Resource Website 1+ mentions |
iMSAT (RRID:SCR_012135) | software resource | A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs. | standalone software, illumina, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25281214 | OMICS_05873 | SCR_012135 | 2026-08-08 11:59:58 | 2 | |||||||||
|
NESmapper Resource Report Resource Website 1+ mentions |
NESmapper (RRID:SCR_012138) | software resource | A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25233087 | GNU General Public License | OMICS_05911 | SCR_012138 | 2026-08-08 11:59:58 | 6 | ||||||||
|
DHAC Resource Report Resource Website 1+ mentions |
DHAC (RRID:SCR_012139) | software resource | Software for clustering time-evolving networks. | standalone software, c++, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22689777 | GNU General Public License | OMICS_05923 | SCR_012139 | Dynamical Hierarchical Agglomerative Clustering | 2026-08-08 12:00:08 | 2 | |||||||
|
MP-EST Resource Report Resource Website 10+ mentions |
MP-EST (RRID:SCR_012145) | software resource | Software that can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species. | standalone software, web app |
is listed by: OMICtools has parent organization: Google Code |
PMID:20937096 | GNU General Public License, v2 | OMICS_06053 | SCR_012145 | Maximum Pseudo-likelihood Estimate of the Species Tree (MP-EST), Maximum Pseudo-likelihood for Estimating Species Trees | 2026-08-08 11:59:58 | 13 | |||||||
|
xMSanalyzer Resource Report Resource Website 50+ mentions |
xMSanalyzer (RRID:SCR_012144) | software resource | A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat. | software package, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23323971 | GNU General Public License | OMICS_06039 | SCR_012144 | 2026-08-08 11:59:41 | 90 | ||||||||
|
LocalAli Resource Report Resource Website 1+ mentions |
LocalAli (RRID:SCR_012147) | software resource | A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:25282642 | GNU General Public License | biotools:localali, OMICS_06337 | https://bio.tools/localali | SCR_012147 | 2026-08-08 11:59:41 | 1 | |||||||
|
OncoSNP-SEQ Resource Report Resource Website 1+ mentions |
OncoSNP-SEQ (RRID:SCR_012742) | OncoSNP-SEQ | software resource | An analytical tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data. | is listed by: OMICtools | OMICS_00348 | SCR_012742 | 2026-08-08 12:00:16 | 6 | ||||||||||
|
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 | 2026-08-08 12:00:02 | 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 | MMDiff - Statistical Testing for ChIP-Seq data sets | 2026-08-08 12:00:02 | 8 | ||||||||
|
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 | 2026-08-08 11:59:44 | 10 | ||||||||||
|
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 | 2026-08-08 11:59:46 | 121 | |||||||||
|
EXCAVATOR-tool Resource Report Resource Website 1+ mentions |
EXCAVATOR-tool (RRID:SCR_012766) | EXCAVATOR-tool | software resource | A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00332 | SCR_012766 | EXCAVATOR-tool: Tool for detecting CNVs from whole-exome sequencing data | 2026-08-08 12:00:16 | 7 | |||||||||
|
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 | RPA: Robust Probabilistic Averaging for probe-level analysis | 2026-08-08 11:59:46 | 1 | |||||||||
|
Isaac Resource Report Resource Website 50+ mentions |
Isaac (RRID:SCR_012772) | Isaac | software resource | Whole genome secondary analysis on Illumina sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:isaac, OMICS_00289 | https://bio.tools/isaac | SCR_012772 | 2026-08-08 11:59:46 | 74 | ||||||||
|
SWIPE Resource Report Resource Website 1+ mentions |
SWIPE (RRID:SCR_012771) | SWIPE | software resource | A software tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. | is listed by: OMICtools | PMID:21631914 | OMICS_00998 | SCR_012771 | Smith-Waterman database searches with inter-sequence SIMD parallelisation | 2026-08-08 12:00:16 | 3 | ||||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | production service resource, web service, software resource, data access protocol, data analysis service, source code, analysis service resource, service resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-08-08 12:00:16 | 10996 |
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