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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IQSeq Resource Report Resource Website 1+ mentions |
IQSeq (RRID:SCR_005238) | IQSeq | software resource | Software for integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework. | is listed by: OMICtools | PMID:22238592 | OMICS_01276 | SCR_005238 | SciCrunch Registry | IQSeq - Integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework | 2026-10-10 12:37:12 | 1 | ||||||||
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ExPANdS Resource Report Resource Website 500+ mentions |
ExPANdS (RRID:SCR_005199) | ExPANdS | software resource | Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results. | copy number, allele, frequency, exome, whole genome, sequencing, ploidy, subpopulation, genotype, mutation, single nucleotide variation |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Tumor | PMID:24177718 | GNU General Public License, v2 | OMICS_00218 | SCR_005199 | SciCrunch Registry | Expanding Ploidy and Allele Frequency on Nested Subpopulations | 2026-10-10 12:37:11 | 907 | |||||
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iReckon Resource Report Resource Website 1+ mentions |
iReckon (RRID:SCR_005232) | iReckon | software resource | An algorithm for the simultaneous isoform reconstruction and abundance estimation. In addition to modelling novel isoforms, multi-mapped reads and read duplicates, this method takes into account the possible presence of unspliced pre-mRNA and intron retention. iReckon only requires a set of transcription start and end sites, but can use known full isoforms to improve sensitivity. Starting from the set of nearly all possible isoforms, iReckon uses a regularized EM algorithm to determine those actually present in the sequenced sample, together with their abundances. iReckon is multi-threaded to increase efficiency in all its time consuming steps. |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:23204306 | OMICS_01277 | SCR_005232 | SciCrunch Registry | 2026-10-10 12:37:12 | 3 | |||||||||
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SnpEff Resource Report Resource Website 5000+ mentions |
SnpEff (RRID:SCR_005191) | SnpEff | software resource | Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. | genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: GATK has parent organization: SourceForge has parent organization: Wayne State University; Michigan; USA works with: SnpSift |
Cancer | PMID:22728672 | Free, Freely available | biotools:snpeff, OMICS_00186 | https://bio.tools/snpeff, https://sources.debian.org/src/snpeff/ | SCR_005191 | SciCrunch Registry | SnpEff - Genetic variant annotation and effect prediction toolbox | 2026-10-10 12:37:01 | 5640 | ||||
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SomaticSniper Resource Report Resource Website 100+ mentions |
SomaticSniper (RRID:SCR_005108) | SomaticSniper | software resource | Software program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 ? 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package. |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
Cancer, Tumor, Normal | PMID:22155872 | Acknowledgement requested | OMICS_00092 | SCR_005108 | SciCrunch Registry | 2026-10-10 12:37:31 | 152 | |||||||
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SimRare Resource Report Resource Website 1+ mentions |
SimRare (RRID:SCR_005226) | SimRare | software resource | A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner. | statistical genetics, simulation framework, gui, association test, sequencing, rare variant, python, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code has parent organization: Baylor University; Texas; USA |
PMID:22914216 | Acknowledgement requested, GNU General Public License, v3 | OMICS_00257, biotools:simrare | https://bio.tools/simrare | SCR_005226 | SciCrunch Registry | SimRare - A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits | 2026-10-10 12:37:12 | 2 | |||||
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SomaticIndelDetector Resource Report Resource Website 50+ mentions |
SomaticIndelDetector (RRID:SCR_005107) | SomaticIndelDetector | software resource | Tool for calling indels in Tumor-Normal paired sample mode. | cancer-specific variant discovery tool, variant, tumor, normal, bam, indel |
is listed by: OMICtools has parent organization: Broad Institute |
Cancer, Tumor, Normal | OMICS_00091 | SCR_005107 | SciCrunch Registry | 2026-10-10 12:37:09 | 82 | ||||||||
|
comrad Resource Report Resource Website 1+ mentions |
comrad (RRID:SCR_005101) | comrad | software resource | A novel algorithmic framework for the integrated analysis of RNA-Seq and Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data. As a result, a Comrad analysis can be performed at a cost comparable to that of two RNA-Seq experiments, significantly lower than an analysis requiring high coverage genome data. | is listed by: OMICtools | Open unspecified license | OMICS_01344 | SCR_005101 | SciCrunch Registry | comrad - Discovery of gene fusions using paired end RNA-Seq and WGSS | 2026-10-10 12:36:59 | 6 | ||||||||
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FlowSim Resource Report Resource Website 1+ mentions |
FlowSim (RRID:SCR_005224) | FlowSim | simulation software, software application, software resource | A suite of tools for simulating the 454 pyrosequencing process. It is based on the characteristics of real 454 data, and attempts to model the known aspects of the process. | is listed by: OMICtools | PMID:20823302 | Acknowledgement requested, GNU General Public License | OMICS_00250 | SCR_005224 | SciCrunch Registry | FlowSim - a simulation pipeline for pyrosequencing data | 2026-10-10 12:37:11 | 2 | |||||||
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PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | SciCrunch Registry | PHAST - PHAge Search Tool | 2026-10-10 12:37:33 | 243 | |||||
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SNPdat Resource Report Resource Website 1+ mentions |
SNPdat (RRID:SCR_005187) | SNPdat | data analysis software, data processing software, software application, software resource | A simple and easy to use high through-put analysis tool which can provide comprehensive annotation of both novel and known single nucleotide polymorphisms (SNPs) for any organism with a draft sequence and annotation. SNPdat makes possible analyses involving non-model organisms that are not supported by the vast majority of SNP annotation tools currently available. It is especially intended for use by researchers with limited bioinformatic experience. | high through-put, single nucleotide polymorphism, annotation, gtf, gff, fasta, sequence analysis, genome, command line |
is listed by: OMICtools has parent organization: Google Code |
PMID:23390980 | GNU General Public License, v2, Acknowledgement requested | OMICS_00184 | SCR_005187 | SciCrunch Registry | SNP Data Analysis Tool, SNPdat - A Simple High Throughput Analysis Tool for Annotating SNPs | 2026-10-10 12:37:00 | 9 | ||||||
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Breakpointer Resource Report Resource Website 10+ mentions |
Breakpointer (RRID:SCR_005254) | Breakpointer | software resource | A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand. | next-generation sequencing, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
GNU General Public License | biotools:breakpointer, OMICS_00308 | https://bio.tools/breakpointer | SCR_005254 | SciCrunch Registry | 2026-10-10 12:37:36 | 10 | |||||||
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CLEVER Toolkit Resource Report Resource Website 10+ mentions |
CLEVER Toolkit (RRID:SCR_005255) | CLEVER Toolkit | software resource | A collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python. | c++, python, structural variation, genome, genotype, linux, unix, windows |
is listed by: OMICtools has parent organization: Google Code |
PMID:23060616 | GNU General Public License, v3 | OMICS_00309 | SCR_005255 | SciCrunch Registry | clever-sv, CLEVER - Clique Enumerating Variant Finder | 2026-10-10 12:37:11 | 35 | ||||||
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Clippers Resource Report Resource Website 1+ mentions |
Clippers (RRID:SCR_005256) | Clippers | software resource | A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format. | long deletion, genome, rna splicing, illumina, deletion |
is listed by: OMICtools is related to: PerM has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 | GNU General Public License, v2, Acknowledgement requested | OMICS_00311 | SCR_005256 | SciCrunch Registry | clippers - Deletion Identification Program using Periodic Spaced Seed | 2026-10-10 12:37:02 | 7 | ||||||
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Moa Resource Report Resource Website |
Moa (RRID:SCR_005373) | Moa | software resource | Software to assist a bioinformatician to organize, document, share, execute and repeat workflows in a command line environment without losing any of the flexibility of the command line, and, at all times giving the user full access to all aspects of the workflow. | command line, workflow, bioinformatics | is listed by: OMICtools | GNU General Public License, v3 | OMICS_01144 | SCR_005373 | SciCrunch Registry | 2026-10-10 12:37:40 | 0 | ||||||||
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AGE Resource Report Resource Website 1+ mentions |
AGE (RRID:SCR_005253) | AGE | software resource | A tool that implements an algorithm for optimal alignment of sequences with Structural Variations (SVs). | genome |
is listed by: OMICtools has parent organization: Yale University; Connecticut; USA |
OMICS_00305 | SCR_005253 | SciCrunch Registry | 2026-10-10 12:37:13 | 3 | |||||||||
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EBIMed Resource Report Resource Website 1+ mentions |
EBIMed (RRID:SCR_005314) | EBIMed | service resource | A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading. | protein, gene, annotation, drug, specie, association, database |
is listed by: OMICtools is related to: MEDLINE is related to: PubMed is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: MedlinePlus has parent organization: European Bioinformatics Institute |
OMICS_01180 | SCR_005314 | SciCrunch Registry | 2026-10-10 12:37:38 | 1 | |||||||||
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Bio-Linux Resource Report Resource Website 10+ mentions |
Bio-Linux (RRID:SCR_005399) | Bio-Linux | software resource | A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux. | ubuntu, cloud computing, workstation, bioinformatics |
is recommended by: NERC Environmental Bioinformatics Centre is listed by: OMICtools has parent organization: Natural Environment Research Council |
PMID:16841067 | Acknowledgement requested, Open unspecified license | OMICS_01137 | SCR_005399 | SciCrunch Registry | BioLinux, NEBC Bio-Linux | 2026-10-10 12:37:41 | 33 | ||||||
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G-Mo.R-Se Resource Report Resource Website 1+ mentions |
G-Mo.R-Se (RRID:SCR_005273) | G-Mo.R-Se | software resource | Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models. | bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01259, biotools:g-mo.r-se, biotools:gmorse | https://bio.tools/g-mo.r-se, https://bio.tools/gmorse | SCR_005273 | SciCrunch Registry | Gene MOdeling using RNA-Seq, G-Mo.R-Se: Gene MOdeling using RNA-Seq | 2026-10-10 12:37:02 | 1 | |||||||
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Binding and Expression Target Analysis Resource Report Resource Website 100+ mentions |
Binding and Expression Target Analysis (RRID:SCR_005396) | BETA | analysis service resource, data analysis service, production service resource, service resource, software resource | A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor''''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor''''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded. | transcription factor, chromatin regulator, transcriptome, chip-seq, cistrome, gene expression, target gene, motif, differential gene expression |
is listed by: OMICtools is related to: Galaxy |
PMID:24263090 | Registration required, Open unspecified license | OMICS_00515 | SCR_005396 | SciCrunch Registry | BETA - Binding and Expression Target Analysis | 2026-10-10 12:37:05 | 455 |
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