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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ABSOLUTE Resource Report Resource Website 100+ mentions |
ABSOLUTE (RRID:SCR_005198) | ABSOLUTE | software resource | Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles. |
is listed by: OMICtools has parent organization: Broad Institute |
Cancer, Normal | PMID:22544022 | Account required | OMICS_00217 | SCR_005198 | 2025-04-19 06:42:46 | 232 | |||||||
|
qSNP Resource Report Resource Website 10+ mentions |
qSNP (RRID:SCR_005105) | qSNP | software resource | A single nucleotide variant caller optimised for identifying somatic variants in low cellularity cancer samples. |
is listed by: OMICtools has parent organization: University of Queensland; Brisbane; Australia |
Cancer | PMID:24250782 | OMICS_00089 | SCR_005105 | 2025-04-19 06:42:44 | 22 | ||||||||
|
Damon Runyon Cancer Research Foundation Resource Report Resource Website 50+ mentions |
Damon Runyon Cancer Research Foundation (RRID:SCR_005106) | Damon Runyon Foundation | institution | The Damon Runyon Cancer Research Foundation funds early career cancer researchers who have the energy, drive and creativity to become leading innovators in their fields. We identify the best young scientists in the nation and support them through four award programs: our Fellowship, Pediatric Cancer Fellowship, Clinical Investigator and Innovation Awards. Damon Runyon awards give young scientists: * Freedom to follow their own ideas, explore new paths and take risks * A prestigious endorsement that attracts further funding, advances their careers and accelerates their research * Guaranteed financial support, sparing them hours applying for grants Since 1946, Damon Runyon has invested more than $240 million in the best young minds in the nation. Our alumni include 11 Nobel Laureates and leaders of major cancer centers across the United States. Many of our 3,300 scientists have gone on to make breakthroughs in the way we prevent, diagnose and treat many forms of cancer. The Damon Runyon Cancer Research Foundation is a registered nonprofit with 501(c)(3) status. | fellowship, grant, cancer | Crossref funder ID: 100001021, grid.453008.a, ISNI: 0000 0004 0508 2172, nlx_144117 | https://ror.org/01gd7b947 | SCR_005106 | 2025-04-19 06:42:44 | 58 | |||||||||
|
SAMtools/BCFtools Resource Report Resource Website 500+ mentions |
SAMtools/BCFtools (RRID:SCR_005227) | BCFtools | software resource | Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | snp, indel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SAMTOOLS |
DOI:10.1101/090811 | biotools:bcftools, OMICS_13458 | https://bio.tools/bcftools https://sources.debian.org/src/bcftools/ |
SCR_005227 | 2025-04-19 06:42:46 | 680 | |||||||
|
MiTie Resource Report Resource Website 1+ mentions |
MiTie (RRID:SCR_005228) | MiTie | software resource | Software framework for simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples. They define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data, and show how to find the optimal solution using Mixed Integer Programming. MiTie can a) take advantage of known transcripts, b) reconstruct and quantify transcripts simultaneously in multiple samples, as well as c) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. | c++, rna-seq, transcript | is listed by: OMICtools | OMICS_01279 | SCR_005228 | MiTie: Simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples | 2025-04-19 06:42:46 | 4 | ||||||||
|
ORMAN Resource Report Resource Website 1+ mentions |
ORMAN (RRID:SCR_005188) | ORMAN | software resource | A software tool for resolving multi-mappings within an RNA-Seq SAM file. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24130305 | OMICS_01284, biotools:orman | https://bio.tools/orman | SCR_005188 | ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms | 2025-04-19 06:42:45 | 4 | ||||||
|
FRCbam Resource Report Resource Website 10+ mentions |
FRCbam (RRID:SCR_005189) | software resource | Software package containing tools to process bam files in order to evaluate and analyze de novo assembly / assemblers and identify Structural Variations suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects. This package contains two tools: # FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers # FindTranslocations: tool to identify chromosomal rearrangements using Mate Pairs | standalone software, sam, bam | is listed by: OMICtools | PMID:23284938 | GNU General Public License, v3 | OMICS_04070 | SCR_005189 | 2025-04-19 06:42:45 | 11 | ||||||||
|
University of KwaZulu-Natal; Durban; South Africa Resource Report Resource Website 1+ mentions |
University of KwaZulu-Natal; Durban; South Africa (RRID:SCR_005222) | UKZN | university | University with five campuses in the province of KwaZulu-Natal in South Africa. It was formed on 1 January 2004 after the merger between the University of Natal and the University of Durban-Westville. |
is parent organization of: Africa Centre Biobank is parent organization of: BioAfrica HIV Informatics in Africa is parent organization of: Africa Centre for Health and Population Studies |
nlx_51412, ISNI:0000 0001 0723 4123, Wikidata:Q727516, grid.16463.36, Crossref funder ID:501100004695 | https://ror.org/04qzfn040 | SCR_005222 | University of KwaZulu-Natal, University of KwaZulu Natal | 2025-04-19 06:42:46 | 3 | ||||||||
|
NGS-SNP Resource Report Resource Website 10+ mentions |
NGS-SNP (RRID:SCR_005182) | NGS-SNP | software resource | A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. | annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line |
is listed by: OMICtools is related to: Ensembl has parent organization: University of Alberta; Alberta; Canada |
OMICS_00177 | SCR_005182 | 2025-04-19 06:42:45 | 31 | |||||||||
|
Indelocator Resource Report Resource Website 10+ mentions |
Indelocator (RRID:SCR_005258) | Indelocator | software resource | A software tool for calling short indels in next generation sequencing data. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00098 | SCR_005258 | 2025-04-19 06:42:47 | 44 | ||||||||||
|
Knime4Bio Resource Report Resource Website 1+ mentions |
Knime4Bio (RRID:SCR_005376) | Knime4Bio | software resource | A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills. | node, next-generation sequencing, knime, bioinformatics, workflow, sequencing, flow, data, bam, wig, bed, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21984761 | GNU General Public License, v3 | biotools:knime4bio, OMICS_01143 | https://bio.tools/knime4bio | SCR_005376 | Knime4Bio: custom nodes for the interpretation of Next Generation Sequencing data with KNIME | 2025-04-19 06:42:50 | 2 | |||||
|
Ergatis Resource Report Resource Website 1+ mentions |
Ergatis (RRID:SCR_005377) | Ergatis | software resource | A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level. | workflow, bioinformatics, workflow management, pipeline, computation, genomics, genome, processing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:20413634 | Artistic License | OMICS_01140 | SCR_005377 | ergatis: workflow creation and monitoring interface | 2025-04-19 06:42:50 | 2 | ||||||
|
CREST Resource Report Resource Website 10+ mentions |
CREST (RRID:SCR_005257) | CREST | software resource | An algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. CREST uses pieces of DNA called soft clips to find structural variations. Soft clips are the DNA segments produced during sequencing that fail to properly align to the reference genome as the sample genome is reassembled. CREST uses the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted. | genome, structural variation, next-generation sequencing, soft clip |
is listed by: OMICtools has parent organization: Pennsylvania State University |
PMID:21666668 | OMICS_00312 | SCR_005257 | 2025-04-19 06:42:47 | 42 | ||||||||
|
PhenoMan Resource Report Resource Website 1+ mentions |
PhenoMan (RRID:SCR_005249) | PhenoMan | software resource | An interactive software program that integrates phenotypic data exploration, selection, management and quality control using a unified platform for association studies of rare and common variants. | phenotype, quality control, statistical genetics, association study, python, 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 |
GNU General Public License, v3 | biotools:phenoman, OMICS_00301 | https://bio.tools/phenoman | SCR_005249 | phenoman - Phenotypic data exploration selection management and quality control for association studies of rare and common variants | 2025-04-19 06:42:47 | 1 | ||||||
|
BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2025-04-19 06:42:51 | 10 | ||||||
|
KGGSeq Resource Report Resource Website 50+ mentions |
KGGSeq (RRID:SCR_005311) | KGGSeq | software resource | A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data. | genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Monogenic disorder, Cancer | PMID:22241780 | biotools:kggseq, OMICS_02260 | https://bio.tools/kggseq | SCR_005311 | KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data | 2025-04-19 06:42:48 | 53 | |||||
|
SOAPindel Resource Report Resource Website 10+ mentions |
SOAPindel (RRID:SCR_005272) | SOAPindel | software resource | Software focusing on calling indels from the next-generation paired-end sequencing data. | is listed by: OMICtools | PMID:22972939 | OMICS_00099 | SCR_005272 | 2025-04-19 06:42:47 | 44 | |||||||||
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PING Resource Report Resource Website 50+ mentions |
PING (RRID:SCR_005394) | PING | software resource | Software program for probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. | clustering, sequencing, statistics, visualization, chip-seq, short-read |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License v2 | OMICS_00513 | http://www.nitrc.org/projects/ping | SCR_005394 | Probabilistic inference for Nucleosome Positioning, PING - Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data | 2025-04-19 06:42:50 | 67 | ||||||
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Scripture Resource Report Resource Website 10+ mentions |
Scripture (RRID:SCR_005269) | Scripture | software resource | Software for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling. | transcriptome, rna-seq read, genome sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Alt Event Finder has parent organization: Broad Institute |
PMID:20436462 | biotools:scripture, OMICS_01265 | https://bio.tools/scripture | SCR_005269 | 2025-04-19 06:42:47 | 11 | |||||||
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NBIA Disorders Association Resource Report Resource Website 1+ mentions |
NBIA Disorders Association (RRID:SCR_005382) | NBIA Disorders Association | institution | The NBIA Disorders Association, formerly known as Hallervorden-Spatz Syndrome Association, (HSSA) was originally founded in 1996 by President, Patricia Wood. The goals of the association are to raise funds to support research pertinent to NBIA; to provide emotional support to those afflicted with NBIA and their families; and to raise public awareness of NBIA. The NBIA Disorders Association is accepting applications for one-year grants for clinical and translational research studies related to the early detection, diagnosis, or treatment of patients with NBIA. Neurodegeneration with Brain Iron Accumulation (NBIA) is a group of rare, genetic, neurological disorders characterized by the accumulation of iron deposits in the brain and progressive degeneration of the nervous system. It typically first appears in childhood. Presenting signs and symptoms may include difficulty walking, loss of balance, and problems related to speech. Those affected suffer a progressive loss of muscle control, sudden involuntary muscle spasms, and uncontrolled tightening of the muscles. Symptoms may also include disorientation, seizures, and deterioration of intellectual ability. Approximately half of the cases diagnosed have been linked to a mutation of a gene known as PANK2. At the present time, symptoms may be treated but there is no cure. The purpose of the NBIA Disorders Association Research Grant Program is to encourage meritorious research studies designed to improve the diagnosis or treatment of NBIA. The research can be conducted in the United States, countries of the European Union, Canada, Australia, New Zealand, Brazil, Argentina, Chile, South Africa, Japan, or Israel, and in other countries where adequate supervision of grant administration is possible. Grants will be awarded to qualified researchers to initiate pilot studies, the results of which are intended to be used to obtain larger multi-year grant funding. Evaluation of proposals will follow NIH guidelines and include careful consideration of experimental or protocol design, objectivity or relevance of parameters measured, and statistical analysis plan. Proposals that address the following areas will be given priority: * Therapeutics Development: ** Development of pantethine and its derivatives ** Development of other rational therapeutics * Animal & Cellular Models: ** Development of a new rodent disease model by targeted insertion of a ''human disease'' mutation into Pank2 ** Development of induced pluripotent stem cell lines. *** Development of animal and cellular models will be considered for multi-year funding with adequate budget justification. Proposals should detail a research plan and a budget for the initial phase of the work, with the option to contract further work out to a commercial enterprise. * Biomarker Discovery and Assay Development: ** Metabolomics ** Coenzyme A / acyl coenzyme A measurement using accessible (peripheral and central) tissue/fluid * New NBIA gene discovery | hallervorden-spatz disease, neurodegeneration with brain iron accumulation, rare disease, pantothenate kinase-associated neurodegeneration, genetic, neurological disorder, brain, neurodegeneration, pank2 | Crossref funder ID: 100009582, grid.469792.7, nlx_144453 | https://ror.org/008421332 | SCR_005382 | NBIA Disorders Association: from discovery to cure, Hallervorden-Spatz Syndrome Association, HSSA | 2025-04-19 06:42:50 | 4 |
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