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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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miR-PREFeR Resource Report Resource Website 1+ mentions |
miR-PREFeR (RRID:SCR_003353) | software resource | An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24930140 | Free, Available for download, Freely available | biotools:mir-prefer, OMICS_04637 | https://bio.tools/mir-prefer | SCR_003353 | miRNA PREdiction From small RNA-Seq data, miR-PREFeR: microRNA PREdiction From small RNAseq data | 2026-08-01 12:02:29 | 7 | ||||||
|
PicTar Resource Report Resource Website 1000+ mentions |
PicTar (RRID:SCR_003343) | PicTar | software resource | An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets | microrna target, microrna, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:15806104 | Free, Available for download, Freely available | OMICS_00411, biotools:pictar, nif-0000-31983 | http://pictar.mdc-berlin.de/, https://bio.tools/pictar | SCR_003343 | 2026-08-01 12:02:20 | 1636 | ||||||
|
BlockClust Resource Report Resource Website 1+ mentions |
BlockClust (RRID:SCR_003347) | software resource | Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. | is listed by: OMICtools | PMID:24931994 | Free, Available for download, Freely available | OMICS_04641 | SCR_003347 | 2026-08-01 12:02:09 | 1 | |||||||||
|
GEOSS Resource Report Resource Website 1+ mentions |
GEOSS (RRID:SCR_003401) | GEOSS | software resource | A complete software system used to store and analyze gene expression data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Virginia; Virginia; USA |
Free, Freely available | OMICS_00764 | SCR_003401 | Gene Expression Open Source System, GEOSS - Gene Expression Open Source System, GEOSS Gene Expression Open Source System, GeneX Va | 2026-08-01 12:02:20 | 1 | ||||||||
|
Assembly Based ReAligner Resource Report Resource Website 1+ mentions |
Assembly Based ReAligner (RRID:SCR_003277) | ABRA | software resource | Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular). | standalone software, c, c++, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24907369 | Free, Available for download, Freely available | OMICS_04668, biotools:abra | https://bio.tools/abra | SCR_003277 | ABRA - Assembly Based ReAligner | 2026-08-01 12:02:29 | 7 | |||||
|
NormqPCR Resource Report Resource Website 50+ mentions |
NormqPCR (RRID:SCR_003388) | NormqPCR | software resource | Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data. | gene expression, microtitre plate assay, qpcr, reference gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22748112 | Free, Available for download, Freely available | OMICS_02315, biotools:normqpcr | https://bio.tools/normqpcr | SCR_003388 | NormqPCR - Functions for normalisation of RT-qPCR data | 2026-08-01 12:02:20 | 51 | |||||
|
BestKeeper Resource Report Resource Website 1000+ mentions |
BestKeeper (RRID:SCR_003380) | BestKeeper | software resource | Excel-based tool using pair-wise correlations for determination of stable housekeeping genes, differentially regulated target genes and sample integrity. It determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points. | gene, excel, quantification, rt-qpcr, gene expression, target gene, differential expression |
is used by: RefFinder is listed by: OMICtools has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:15127793 | Free, Available for download, Freely available | OMICS_02318 | http://bestkeeper.gene-quantification.info/ | http://www.wzw.tum.de/gene-quantification/bestkeeper.html | SCR_003380 | 2026-08-01 12:02:10 | 1126 | |||||
|
Amplicon Resource Report Resource Website 1000+ mentions |
Amplicon (RRID:SCR_003294) | Amplicon | software resource | Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac | python, pcr primer, pcr, primer, tkinter, windows, dna sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:14962918 | Free, Available for download, Freely available | OMICS_02329 | http://www.aad.gov.au/amplicon | SCR_003294 | 2026-08-01 12:02:19 | 1673 | ||||||
|
Nestly Resource Report Resource Website |
Nestly (RRID:SCR_003472) | Nestly | software resource | A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. | python | is listed by: OMICtools | PMID:23220574 | MIT License | OMICS_02300 | SCR_003472 | 2026-08-01 12:02:31 | 0 | |||||||
|
PoPoolation Resource Report Resource Website 100+ mentions |
PoPoolation (RRID:SCR_003495) | PoPoolation | software resource | A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. | population genetics, next generation sequencing, sliding window, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21253599 | Acknowledgement requested | OMICS_04414, biotools:popoolation | https://bio.tools/popoolation | SCR_003495 | 2026-08-01 12:02:13 | 139 | ||||||
|
JISTIC Resource Report Resource Website 1+ mentions |
JISTIC (RRID:SCR_003482) | JISTIC | software resource | Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. | copy number variation, candidate gene, gene |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
Cancer | PMID:20398270 | Free, Public | OMICS_02297 | SCR_003482 | 2026-08-01 12:02:13 | 2 | ||||||
|
MetABEL Resource Report Resource Website 1+ mentions |
MetABEL (RRID:SCR_003429) | MetABEL | software resource | Software for meta-analysis of genome-wide SNP association results. | is listed by: OMICtools | PMID:17384015 | Free, Available for download, Freely available | OMICS_00237 | https://www.rdocumentation.org/packages/MetABEL/versions/0.2-0 | SCR_003429 | 2026-08-01 12:02:30 | 6 | |||||||
|
LaSSO Resource Report Resource Website 100+ mentions |
LaSSO (RRID:SCR_003418) | software resource | An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns. | standalone software, r, FASEB list | is listed by: OMICtools | PMID:24709818 | Free, Available for download, Freely available | OMICS_04622 | SCR_003418 | Lariat Sequence Site Origin | 2026-08-01 12:02:11 | 157 | |||||||
|
metaphor Resource Report Resource Website 100+ mentions |
metaphor (RRID:SCR_003450) | metaphor | software resource | A free and open-source add-on for conducting meta-analyses with the statistical software environment R. | is listed by: OMICtools | GNU General Public License, v2 | OMICS_00240 | SCR_003450 | The metafor package, The metafor package: A meta-analysis package for R | 2026-08-01 12:02:21 | 311 | ||||||||
|
SWAN Resource Report Resource Website 100+ mentions |
SWAN (RRID:SCR_003455) | SWAN | software resource | Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package. | dna methylation, microarray |
is listed by: OMICtools is related to: minfi has parent organization: Bioconductor |
PMID:22703947 | Free, Available for download, Freely available | OMICS_02303 | SCR_003455 | Subset-quantile Within Array Normalization | 2026-08-01 12:02:21 | 190 | ||||||
|
BMIQ Resource Report Resource Website 100+ mentions |
BMIQ (RRID:SCR_003446) | BMIQ | software resource | Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. | illumina infinium 450k, dna methylation, probe design, normalization |
is listed by: OMICtools has parent organization: Google Code |
PMID:23175756 | Free, Available for download, Freely available | OMICS_02304 | https://aeteschendorff-lab.github.io/software/BMIQ/ | SCR_003446 | bmiq - Beta Mixture Quantile Model, Beta MIxture Quantile dilation | 2026-08-01 12:02:12 | 125 | |||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | Genome Expression Pathway Analysis Tool | 2026-08-01 12:02:15 | 2 | ||||||
|
Osprey Resource Report Resource Website 10+ mentions |
Osprey (RRID:SCR_003627) | Osprey | software resource | Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Calgary; Alberta; Canada |
PMID:15456895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00832 | SCR_003627 | Osprey: Oligonucleotide Design Software | 2026-08-01 12:02:32 | 47 | |||||||
|
UEA sRNA toolkit Resource Report Resource Website 10+ mentions |
UEA sRNA toolkit (RRID:SCR_003620) | UEA sRNA toolkit | software resource | Software tools for the analysis of high-throughput small RNA data. | is listed by: OMICtools | PMID:22628521 | OMICS_00369 | SCR_003620 | 2026-08-01 12:02:23 | 32 | |||||||||
|
RINS Resource Report Resource Website 10+ mentions |
RINS (RRID:SCR_003652) | RINS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only. | virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perl |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22377895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00223 | SCR_003652 | 2026-08-01 12:02:32 | 26 |
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