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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
AS-Peak Resource Report Resource Website 1+ mentions |
AS-Peak (RRID:SCR_000380) | ASPeak | software resource | A software that utilizes a peak detection algorithm to identify RNA-protein binding sites. | rna, peak detection, protein, binding, site, algorithm, analysis |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23929032 | Free, Available for download, Freely available | OMICS_00566 | https://omictools.com/aspeak-tool | SCR_000380 | 2026-07-25 12:04:43 | 2 | ||||||
|
TargetCaller Resource Report Resource Website |
TargetCaller (RRID:SCR_000414) | TargetCaller | software resource | R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only). | chip-seq, transcription factor, target gene |
is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
PMID:24278002 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01807 | SCR_000414 | 2026-07-25 12:04:44 | 0 | |||||||
|
bzip2 Resource Report Resource Website |
bzip2 (RRID:SCR_000376) | bzip2 | software resource | A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface. | data, compression, decompression, gui, programming, interface | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00951 | SCR_000376 | 2026-07-25 12:04:44 | 0 | ||||||||
|
flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-07-25 12:04:44 | 21 | |||||||
|
Flicker Resource Report Resource Website |
Flicker (RRID:SCR_000288) | software resource | An open-source stand-alone computer program for visually comparing 2D gel images. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:10027264 | Free, Available for download, Freely available | OMICS_02538, biotools:nci_flicker | https://bio.tools/nci_flicker | SCR_000288 | 2026-07-25 12:04:41 | 0 | |||||||
|
OMSSAPercolator Resource Report Resource Website |
OMSSAPercolator (RRID:SCR_000287) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24504981 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02524 | SCR_000287 | 2026-07-25 12:04:42 | 0 | ||||||||
|
OLINgui Resource Report Resource Website |
OLINgui (RRID:SCR_000435) | OLINgui | software resource | Software package providing a graphical user interface for the OLIN package. | microarray, preprocessing, quality control, two channel, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:olingui, OMICS_02030 | https://bio.tools/olingui | SCR_000435 | OLINgui - Graphical user interface for OLIN | 2026-07-25 12:04:45 | 0 | ||||||
|
ArrayPlex Resource Report Resource Website |
ArrayPlex (RRID:SCR_000312) | ArrayPlex | software resource | Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture. | microarray, programmatic framework, collaborative, client-server, |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19014503 | Free, Available for download, Freely available | OMICS_00745 | SCR_000312 | 2026-07-25 12:04:42 | 0 | |||||||
|
MeQA Resource Report Resource Website |
MeQA (RRID:SCR_000317) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data. | quality assessment, read distribution, methylation estimation, medip, medip-sequence, dna methylation, utilities tool, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tongji University; Shanghai; China |
PMID:22199384 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:meqa, OMICS_00616 | https://bio.tools/meqa | SCR_000317 | 2026-07-25 12:04:43 | 0 | |||||||
|
Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | microAnalyzer | 2026-07-25 12:04:44 | 0 | |||||
|
FunctSNP Resource Report Resource Website |
FunctSNP (RRID:SCR_000393) | FunctSNP | software resource | An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge. | single nucleotide polymorphism |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20534127 | Free, Available for download, Freely available | OMICS_01925 | SCR_000393 | FunctSNP - Linking SNPs to functional knowledge | 2026-07-25 12:04:43 | 0 | ||||||
|
flowStats Resource Report Resource Website |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-07-25 12:04:45 | 0 | ||||||||
|
d2-tools Resource Report Resource Website |
d2-tools (RRID:SCR_000425) | software resource | Software toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity. | standalone software, python, r |
is listed by: OMICtools has parent organization: Google Code |
PMID:24392128 | Free, Freely available | OMICS_02621 | SCR_000425 | 2026-07-25 12:04:44 | 0 | ||||||||
|
Clonality Resource Report Resource Website |
Clonality (RRID:SCR_000293) | Clonality | software resource | Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles. | classification, copy number variant, microarray, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02059 | SCR_000293 | Clonality - Clonality testing | 2026-07-25 12:04:42 | 0 | |||||||
|
RADtools Resource Report Resource Website 1+ mentions |
RADtools (RRID:SCR_000324) | software resource | Software tools for processing RAD Sequencing Illumina reads. Version 1.0 is a pipeline for transforming Illumina reads into candidate genetic markers. | standalone software, illumina | is listed by: OMICtools | PMID:21541297 | Free, Available for download, Freely available | OMICS_03727 | https://www.wiki.ed.ac.uk/display/RADSequencing/ | SCR_000324 | 2026-07-25 12:04:42 | 1 | |||||||
|
NIMBL Resource Report Resource Website 1+ mentions |
NIMBL (RRID:SCR_000482) | NIMBL | software resource | MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays. | quality control, illumina, infinium array, dna methylation, biomarker, dna methylation array, dna methylome, infinium 450k, biomarker discovery, differential methylation, epigenetics, epigenomics |
is listed by: OMICtools has parent organization: University of Nottingham; Nottingham; United Kingdom |
PMID:22936948 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02305 | SCR_000482 | NIMBL: Numerical Identification of Methylation Biomarker Lists, Numerical Identification of Methylation Biomarker Lists | 2026-07-25 12:04:47 | 1 | ||||||
|
iBMQ Resource Report Resource Website |
iBMQ (RRID:SCR_000481) | software resource | Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. | standalone software, mac os x, unix/linux, windows, r, gene expression, microarray, preprocessing, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23958729 | Free, Available for download, Freely available | OMICS_04601 | SCR_000481 | iBMQ - integrated Bayesian Modeling of eQTL data | 2026-07-25 12:04:46 | 0 | |||||||
|
fourSig Resource Report Resource Website |
fourSig (RRID:SCR_000516) | software resource | A suite of software programs for analyzing and visualizing 4C-seq data. | standalone software, perl, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24561615 | Free, Available for download, Freely available | OMICS_02628 | SCR_000516 | 2026-07-25 12:04:46 | 0 | ||||||||
|
SAMBLASTER Resource Report Resource Website 10+ mentions |
SAMBLASTER (RRID:SCR_000468) | software resource | Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
PMID:24812344 DOI:10.1093/bioinformatics/btu314 |
Free, Available for download, Freely available | biotools:samblaster, OMICS_04682 | https://bio.tools/samblaster, https://sources.debian.org/src/samblaster/ | SCR_000468 | 2026-07-25 12:04:46 | 18 | |||||||
|
TAPyR Resource Report Resource Website 1+ mentions |
TAPyR (RRID:SCR_000588) | software resource | An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies. | gs flx, genome analyzer, bwt, fasta, fastq, sff formats, pyrosequencing reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21672185 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tapyr, OMICS_00693 | https://bio.tools/tapyr | SCR_000588 | Tool for Alignment of Pyrosequencing Reads | 2026-07-25 12:04:48 | 1 |
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