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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
QSRA Resource Report Resource Website 1+ mentions |
QSRA (RRID:SCR_010733) | QSRA | software resource | A quality-value guided de novo short read assembler. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00026, biotools:qsra | https://bio.tools/qsra | SCR_010733 | 2026-08-08 11:59:35 | 1 | ||||||||
|
rSW-seq Resource Report Resource Website 1+ mentions |
rSW-seq (RRID:SCR_010825) | rSW-seq | software resource | Designed to identify CNVs between two genomes. | is listed by: OMICtools | PMID:20718989 | OMICS_00351 | SCR_010825 | 2026-08-08 11:59:37 | 4 | |||||||||
|
SegSeq Resource Report Resource Website 10+ mentions |
SegSeq (RRID:SCR_010826) | SegSeq | software resource | An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00352 | SCR_010826 | 2026-08-08 11:59:37 | 20 | ||||||||||
|
miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | Helmholtz-Alliance on Systems Biology ; Helmholtz Association ; German Ministry of Education and Research ; Senate of Berlin ; China Scholarship Council ; Max Delbrück Centrum Systems Biology Network |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-08-08 11:59:37 | 182 | |||||
|
SAPRED Resource Report Resource Website 1+ mentions |
SAPRED (RRID:SCR_010785) | SAPRED | software resource | Offers the researchers an automatic pipeline to predict the disease-association of SAPs. |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:17384424 | OMICS_00161 | SCR_010785 | SAP Disease-Association Predictor | 2026-08-08 11:59:36 | 4 | ||||||||
|
SNAP - Effects of Single Amino Acid Substitutions on Protein Function Resource Report Resource Website 10+ mentions |
SNAP - Effects of Single Amino Acid Substitutions on Protein Function (RRID:SCR_010786) | SNAP | production service resource, software resource, data analysis service, analysis service resource, service resource | A method for evaluating effects of single amino acid substitutions on protein function. |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
PMID:17526529 | Acknowledgement requested | OMICS_00162 | SCR_010786 | 2026-08-08 11:59:24 | 38 | ||||||||
|
TransFIC Resource Report Resource Website 10+ mentions |
TransFIC (RRID:SCR_010788) | TransFIC | production service resource, software resource, data analysis service, software application, analysis service resource, data analysis software, service resource, data processing software | A method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes. |
is listed by: OMICtools has parent organization: Pompeu Fabra University; Barcelona; Spain |
Cancer | OMICS_00164 | SCR_010788 | TRANSformed Functional Impact for Cancer | 2026-08-08 11:59:36 | 14 | ||||||||
|
JointSLM Resource Report Resource Website 1+ mentions |
JointSLM (RRID:SCR_010823) | JointSLM | software resource | Copy number estimation from read depth information. | is listed by: OMICtools | OMICS_00346 | SCR_010823 | 2026-08-08 11:59:37 | 2 | ||||||||||
|
EMINIM Resource Report Resource Website 1+ mentions |
EMINIM (RRID:SCR_010790) | EMINIM | software resource | A software tool for imputation of unobserved genotypes using a set of reference haplotype panel at a higher-density SNP set such as HapMap, and lower-density genotypes of a target individual using such as genotyping arrays. |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
OMICS_00196 | SCR_010790 | Expectation-Maximized INtegreative Imputation, Expectation-Maximized INtegreative IMputation (EMINIM) | 2026-08-08 11:59:24 | 1 | |||||||||
|
HARSH Resource Report Resource Website 10+ mentions |
HARSH (RRID:SCR_010792) | HARSH | software resource | Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
OMICS_00199, biotools:harsh | https://bio.tools/harsh | SCR_010792 | HAplotype inference using Reference and Sequencing tecHnology | 2026-08-08 11:59:36 | 15 | |||||||
|
HapFABIA Resource Report Resource Website 1+ mentions |
HapFABIA (RRID:SCR_010793) | HapFABIA | software resource | Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:24174545 | biotools:hapfabia, OMICS_00203 | https://bio.tools/hapfabia | SCR_010793 | HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data | 2026-08-08 11:59:24 | 3 | ||||||
|
C-mii Resource Report Resource Website 1+ mentions |
C-mii (RRID:SCR_010839) | C-mii | software resource | A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed. | ubuntu linux, windows | is listed by: OMICtools | PMID:23281648 | GNU General Public License | OMICS_00394 | SCR_010839 | C-mii: A software for Computational miRNA identificaion, C-mii (A software for Computational miRNA identificaion) | 2026-08-08 11:59:38 | 4 | ||||||
|
Pedimap Resource Report Resource Website 10+ mentions |
Pedimap (RRID:SCR_010796) | Pedimap | software resource | A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23087384 | OMICS_00214, biotools:pedimap | https://bio.tools/pedimap | SCR_010796 | 2026-08-08 11:59:36 | 11 | |||||||
|
Phylogeny Programs Resource Report Resource Website 10+ mentions |
Phylogeny Programs (RRID:SCR_010797) | Phylogeny Programs | data or information resource, production service resource, software resource, data analysis service, topical portal, analysis service resource, service resource, portal | 392 phylogeny software packages and 54 free web servers describing all known software for inferring phylogenies (evolutionary trees). Submissions are welcome. Programs are listed by methods available, by computer systems on which they work, cross-referenced by method and by computer system, by ones which analyze particular kinds of data, to show the most recent listings, or to show ones most recently changed. | phylogeny |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NSF | Free, The community can contribute to this resource | OMICS_00219 | SCR_010797 | Felsenstein''s website | 2026-08-08 11:59:24 | 13 | ||||||
|
NHLBI Grand Opportunity Exome Sequencing Project Resource Report Resource Website 10+ mentions |
NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) | NHLBI GO ESP, GO ESP | knowledge environment | Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations. | next-generation sequencing, protein coding region, human, genome, phenotype, exome sequencing |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NHLBI RC2 HL-103010; NHLBI RC2 HL-102923; NHLBI RC2 HL-102924; NHLBI RC2 HL-102925; NHLBI RC2 HL-102926 |
OMICS_00277 | SCR_010798 | NHLBI Grand Opportunity Exome Sequencing Project (ESP), NHLBI GO Exome Sequencing Project (ESP) | 2026-08-08 11:59:36 | 35 | |||||||
|
miRspring Resource Report Resource Website 1+ mentions |
miRspring (RRID:SCR_010832) | miRspring | software resource | Pipeline scripts for creating a miRspring (miRNA sequence profiling) document, a new way of sharing and analysing sequencing data for small RNA. |
is listed by: OMICtools has parent organization: Victor Chang Cardiac Research Institute; New South Wales; Australia |
OMICS_00382 | SCR_010832 | miRNA sequence profiling (miRspring) document, miRspring document, miRNA sequence profiling | 2026-08-08 11:59:37 | 1 | |||||||||
|
ShortStack Resource Report Resource Website 100+ mentions |
ShortStack (RRID:SCR_010834) | software resource | A software tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes. ShortStack discovers small RNA ''clusters'' de novo, based on user-set thresholds, and annotates clusters with respect to small RNA size, orientation, and repetitiveness. ShortStack also discovers and annotates MIRNA genes, and other Hairpin-associated small RNA genes. In addition, ShortStack includes a robust method to detect genes producing small RNAs in a phased manner. It outputs a descriptive table of all results, useful genome browser tracks, a table describing the results of the hairpin / MIRNA analysis for each cluster, and detailed text-based alignments of all MIRNAs and hairpin-associated clusters. It can also be run in ''count'' mode, to quantify a set of input loci with genomic coordinates determined a priori by the user. ShortStack is a perl program. Besides perl, ShortStack also requires samtools and the RNALfold and RNAeval programs from the Vienna RNA Package to execute. When used to control the alignment of small RNA data to a reference genome, ShortStack also requires bowtie and bowtie-build. Finally, for optimal results, ShortStack uses a file of inverted repeats produced by the EMBOSS application einverted. |
is listed by: OMICtools has parent organization: Pennsylvania State University |
PMID:24139974 PMID:23610128 |
Acknowledgement requested | OMICS_00384 | http://axtell-lab-psu.weebly.com/shortstack.html | SCR_010834 | ShortStack : Comprehensive annotation and quantification of small RNA genes | 2026-08-08 11:59:37 | 235 | |||||||
|
reseqtools Resource Report Resource Website 10+ mentions |
reseqtools (RRID:SCR_010806) | reseqtools | software resource | A Toolkit for analyzing next-generation DNA Re-Sequencing data. | java, unix/linux |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_00293 | SCR_010806 | 2026-08-08 11:59:24 | 18 | ||||||||
|
TREAT Resource Report Resource Website 10+ mentions |
TREAT (RRID:SCR_010808) | TREAT | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Targeted RE-sequencing Annotation Tool that offers a comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00295 | SCR_010808 | 2026-08-08 11:59:36 | 49 | |||||||||
|
GAMES Resource Report Resource Website 100+ mentions |
GAMES (RRID:SCR_010762) | GAMES | software resource | Software that identifies and annotates mutations in next-generation sequencing projects. | is listed by: OMICtools | OMICS_00060 | SCR_010762 | 2026-08-08 11:59:35 | 119 |
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