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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
AllSeq Resource Report Resource Website |
AllSeq (RRID:SCR_010053) | AllSeq | service resource | Free online tools to find the best Sequencing Service provider for your project. | is listed by: OMICtools | Free | OMICS_01726 | SCR_010053 | 2026-02-14 02:01:53 | 0 | |||||||||
|
IsoEM Resource Report Resource Website 10+ mentions |
IsoEM (RRID:SCR_009993) | IsoEM | software resource | Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Connecticut; Connecticut; USA |
biotools:isoem, OMICS_01278 | https://bio.tools/isoem | SCR_009993 | 2026-02-14 02:01:43 | 10 | ||||||||
|
BitSeq Resource Report Resource Website 10+ mentions |
BitSeq (RRID:SCR_009904) | BitSeq | software resource | A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btv483 DOI:10.1093/bioinformatics/bts260 |
, OMICS_01269, biotools:bitseq | https://bio.tools/bitseq https://sources.debian.org/src/bitseq/ |
SCR_009904 | 2026-02-14 02:01:42 | 19 | |||||||
|
TrueSight Resource Report Resource Website 1+ mentions |
TrueSight (RRID:SCR_009835) | TrueSight | software resource | Self-training Algorithm for Splice Junction Detection using RNA-seq. | is listed by: OMICtools | OMICS_01258 | SCR_009835 | 2026-02-14 02:01:53 | 2 | ||||||||||
|
ABMapper Resource Report Resource Website 1+ mentions |
ABMapper (RRID:SCR_010242) | ABMapper | software resource | A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts. | is listed by: OMICtools | OMICS_01238 | SCR_010242 | ABMapper: A suffix-array based spliced alignment tool | 2026-02-14 02:01:55 | 1 | |||||||||
|
vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-02-14 02:02:02 | 58 | ||||||||||
|
MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., 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 has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-02-14 02:02:02 | 463 | |||||||
|
Gossamer Resource Report Resource Website 1+ mentions |
Gossamer (RRID:SCR_010612) | Gossamer | software resource | A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. | is listed by: OMICtools | OMICS_00017 | SCR_010612 | Gossamer: A Space-Efficient Genome Assembler | 2026-02-14 02:02:02 | 1 | |||||||||
|
Meraculous Resource Report Resource Website 10+ mentions |
Meraculous (RRID:SCR_010700) | Meraculous | software resource | An algorithm for de novo genome assembly with short paired-end reads. | is listed by: OMICtools | OMICS_00021 | SCR_010700 | Meraculous: De Novo Genome Assembly with Short Paired-End Reads | 2026-02-14 02:02:03 | 39 | |||||||||
|
ContextMap Resource Report Resource Website 10+ mentions |
ContextMap (RRID:SCR_010496) | ContextMap | software resource | A context-based approach to identify the most likely mapping for RNA-seq experiments. | is listed by: OMICtools | OMICS_01239 | SCR_010496 | 2026-02-14 02:01:46 | 27 | ||||||||||
|
CRAC Resource Report Resource Website 10+ mentions |
CRAC (RRID:SCR_010652) | CRAC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1186/s12920-016-0178-5 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01240 | https://sources.debian.org/src/crac/ | SCR_010652 | 2026-02-14 02:01:48 | 16 | |||||||
|
CoRAL - Classification of RNAs by Analysis of Length Resource Report Resource Website 1+ mentions |
CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) | CoRAL | software resource | A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs. |
is listed by: OMICtools has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:23700308 | Acknowledgement requested | OMICS_00372 | SCR_010828 | Classification of RNAs by Analysis of Length | 2026-02-14 02:01:50 | 8 | |||||||
|
PriVar Resource Report Resource Website 1+ mentions |
PriVar (RRID:SCR_010784) | PriVar | software resource | A toolkit for prioritizing SNVs and indels from next-generation sequencing data. | is listed by: OMICtools | OMICS_00160 | SCR_010784 | 2026-02-14 02:02:03 | 2 | ||||||||||
|
CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | 2026-02-14 02:01:50 | 8 | ||||||||
|
CNVnator Resource Report Resource Website 500+ mentions |
CNVnator (RRID:SCR_010821) | CNVnator | software resource | An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. | is listed by: OMICtools | OMICS_00343 | SCR_010821 | 2026-02-14 02:02:04 | 510 | ||||||||||
|
Diplotyper Resource Report Resource Website |
Diplotyper (RRID:SCR_010789) | Diplotyper | software resource | A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00195 | SCR_010789 | 2026-02-14 02:02:03 | 0 | ||||||||||
|
Control-FREEC Resource Report Resource Website 100+ mentions |
Control-FREEC (RRID:SCR_010822) | Control-FREEC | software resource | Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data. | is listed by: OMICtools | OMICS_00344 | SCR_010822 | 2026-02-14 02:02:06 | 327 | ||||||||||
|
readDepth Resource Report Resource Website 10+ mentions |
readDepth (RRID:SCR_010824) | readDepth | software resource | This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. | is listed by: OMICtools | OMICS_00350 | SCR_010824 | 2026-02-14 02:01:50 | 23 | ||||||||||
|
HapCUT Resource Report Resource Website 10+ mentions |
HapCUT (RRID:SCR_010791) | HapCUT | software resource | A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. | is listed by: OMICtools | OMICS_00198 | SCR_010791 | 2026-02-14 02:02:04 | 17 | ||||||||||
|
Relate Resource Report Resource Website 10+ mentions |
Relate (RRID:SCR_010794) | Relate | software resource | Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19025785 | biotools:relateadmix, OMICS_00207 | https://bio.tools/relateadmix | SCR_010794 | 2026-02-14 02:02:06 | 44 |
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