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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NGC Resource Report Resource Website |
NGC (RRID:SCR_009342) | NGC | software resource | A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files. | is listed by: OMICtools | PMID:23066097 | OMICS_00964 | SCR_009342 | 2026-09-12 12:57:12 | 0 | |||||||||
|
iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-09-12 12:57:12 | 11 | ||||||
|
Gecko Resource Report Resource Website 500+ mentions |
Gecko (RRID:SCR_009001) | Gecko | software resource | A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15588317 | OMICS_00758 | SCR_009001 | Gene Expression: Computation and Knowledge Organization, Geckoe | 2026-09-12 12:57:11 | 547 | ||||||||
|
Quip Resource Report Resource Website 50+ mentions |
Quip (RRID:SCR_009362) | Quip | software resource | Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice. | is listed by: OMICtools | OMICS_00965 | SCR_009362 | 2026-09-12 12:57:12 | 56 | ||||||||||
|
MFCompress Resource Report Resource Website 1+ mentions |
MFCompress (RRID:SCR_009301) | MFCompress | software resource | A compression tool for FASTA and multi-FASTA files. | is listed by: OMICtools | PMID:24132931 | OMICS_00963 | SCR_009301 | 2026-09-12 12:57:12 | 3 | |||||||||
|
RLZ Resource Report Resource Website |
RLZ (RRID:SCR_009420) | RLZ | software resource | Optimized relative Lempel-Ziv compression of genomes. | is listed by: OMICtools | OMICS_00966 | SCR_009420 | Relative Lempel-Ziv Compression of Genomes | 2026-09-12 12:57:12 | 0 | |||||||||
|
GReEn Resource Report Resource Website 100+ mentions |
GReEn (RRID:SCR_009264) | GReEn | software resource | A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Aveiro; Aveiro; Portugal |
PMID:23872967 PMID:22139935 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00959 | SCR_009264 | Genome Resequencing Encoding | 2026-09-12 12:57:12 | 346 | |||||||
|
SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, data processing software, software application, software resource | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Health ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-09-12 12:57:14 | 31 | ||||||
|
ISRNA Resource Report Resource Website 1+ mentions |
ISRNA (RRID:SCR_009565) | ISRNA | software resource | An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:24300438 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00360 | SCR_009565 | Integrative Short Reads NAvigator | 2026-09-12 12:57:13 | 3 | |||||||
|
shortran Resource Report Resource Website |
shortran (RRID:SCR_009636) | shortran | software resource | A pipeline for small RNA-seq data analysis. | is listed by: OMICtools | PMID:22914220 | Free | OMICS_00368 | SCR_009636 | 2026-09-12 12:57:14 | 0 | ||||||||
|
SCALCE Resource Report Resource Website |
SCALCE (RRID:SCR_009658) | SCALCE | software resource | A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00969 | SCR_009658 | Boosting Sequence Compression Algorithms using Locally Consistent Encoding | 2026-09-12 12:57:14 | 0 | |||||||||
|
Generic Exome Analysis Plan Resource Report Resource Website |
Generic Exome Analysis Plan (RRID:SCR_009656) | data or information resource, experimental protocol, narrative resource | Outline of a generic plan for analysis of a whole exome sequencing project. |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
nlx_156093 | SCR_009656 | 2026-09-12 12:57:14 | 0 | |||||||||||
|
SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-09-12 12:57:14 | 21 | |||||||
|
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 | 2026-09-12 12:57:15 | 2 | ||||||||||
|
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 | 2026-09-12 12:57:15 | 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 | 2026-09-12 12:57:15 | 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 | 2026-09-12 12:57:15 | 20 | |||||||
|
BEAST Resource Report Resource Website 5000+ mentions |
BEAST (RRID:SCR_010228) | data analysis software, data processing software, sequence analysis software, software application, software repository, software resource | A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. | bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: TempEst is related to: BEAST2 is related to: PhyDyn has parent organization: University of Edinburgh; Scotland; United Kingdom |
DOI:10.1186/1471-2148-7-214 | nlx_156859, OMICS_04233, biotools:beast, SCR_015988 | http://www.nitrc.org/projects/beast-library, https://bio.tools/beast, https://sources.debian.org/src/beast-mcmc/ | http://beast.bio.ed.ac.uk/Main_Page | SCR_010228 | BEaST Segmentation Library, Beast Software | 2026-09-12 12:57:15 | 6777 | ||||||
|
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 | 2026-09-12 12:57:16 | 1 | |||||||||
|
Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-09-12 12:58:19 | 9083 |
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