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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CancerMutationAnalysis Resource Report Resource Website |
CancerMutationAnalysis (RRID:SCR_013181) | CancerMutationAnalysis | software resource | Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer. |
is listed by: OMICtools has parent organization: Bioconductor |
Cancer | OMICS_00141 | SCR_013181 | 2026-09-19 12:52:39 | 0 | |||||||||
|
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 | 2026-09-19 12:52:40 | 38 | ||||||
|
AcroMine Resource Report Resource Website |
AcroMine (RRID:SCR_013196) | data access protocol, service resource, software resource, web service | An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. | acronym, abbreviation, disambiguation, computational linguistics, text mining |
is listed by: FORCE11 is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
JISC ; BBSRC ; EPSRC |
PMID:20360059 PMID:17050571 |
Free, Public | OMICS_01169, nif-0000-10215 | SCR_013196 | Acromine | 2026-09-19 12:52:39 | 0 | ||||||
|
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 | 2026-09-19 12:52:39 | 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 | 2026-09-19 12:52:39 | 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 | 2026-09-19 12:52:39 | 68 | ||||||||||
|
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 | 2026-09-19 12:52:41 | 4 | ||||||||||
|
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 | 2026-09-19 12:52:41 | 72 | ||||||||
|
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 | 2026-09-19 12:52:41 | 5 | ||||||||
|
Probalign Resource Report Resource Website 10+ mentions |
Probalign (RRID:SCR_013332) | Probalign | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats. |
is used by: eProbalign is listed by: OMICtools is listed by: Debian has parent organization: New Jersey Institute of Technology; New Jersey; USA |
PMID:16954142 DOI:10.1093/bioinformatics/btl472 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00985 | https://sources.debian.org/src/probalign/ | SCR_013332 | Probalign: multiple sequence alignment using partition function posterior probabilities | 2026-09-19 12:52:41 | 16 | ||||||
|
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 | 2026-09-19 12:52:42 | 125 | ||||||||||
|
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 | 2026-09-19 12:52:43 | 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 | 2026-09-19 12:52:43 | 2754 | ||||||||
|
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 | 2026-09-19 12:52:43 | 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 | 2026-09-19 12:52:41 | 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 | 2026-09-19 12:52:41 | 119 | |||||||||
|
caArray Resource Report Resource Website 10+ mentions |
caArray (RRID:SCR_006053) | caArray | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management. | microarray, gene expression, data sharing, service resource, data management, annotation, interoperability, life sciences |
is listed by: re3data.org is listed by: OMICtools is related to: Cancer Biomedical Informatics Grid is related to: MAGE-TAB has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151452, OMICS_00864, r3d100010573 | https://doi.org/10.17616/R33G76 | SCR_006053 | caArray - Array Data Management System, caArray Data Portal | 2026-09-19 12:51:03 | 35 | |||||
|
MetaQC Resource Report Resource Website 10+ mentions |
MetaQC (RRID:SCR_006000) | software resource | Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. | standalone software, mac os x, unix/linux, windows, r, FASEB list |
is listed by: OMICtools has parent organization: CRAN |
PMID:22116060 | GNU General Public License, v2 | OMICS_04032 | https://github.com/donkang34/MetaQC | SCR_006000 | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis | 2026-09-19 12:51:03 | 40 | ||||||
|
DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | data or information resource, data repository, database, service resource, storage service resource | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; Scientific Research Fund of Heilongjiang Provincial Education Department ; State Key Laboratory of Urban Water Resource and Environment |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth, https://bio.tools/diseasemeth | http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-09-19 12:51:02 | 44 | ||||
|
BLESS Resource Report Resource Website 10+ mentions |
BLESS (RRID:SCR_005963) | BLESS | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory. | c++, next-generation sequencing, bloom-filter, error correction, ngs, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24451628 | GNU General Public License v3 | OMICS_02246, biotools:bless | https://bio.tools/bless | SCR_005963 | BLoom-filter-based Error correction Solution for high-throughput Sequencing reads, BLESS - Bloom-filter-based Error Correction Tool for NGS reads | 2026-09-19 12:51:02 | 46 |
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