Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software toolkit, software resource | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer, https://bio.tools/khmer, https://sources.debian.org/src/khmer/ | https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-07-28 09:40:08 | 25 | ||||
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, standalone software, software resource | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
NCI CA009363; NCI CA138249; NHGRI HG006853; Edelman-Gardner Foundation |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-07-28 09:40:22 | 1 | |||||
|
Berkeley Drosophila Genome Project Resource Report Resource Website 100+ mentions |
Berkeley Drosophila Genome Project (RRID:SCR_013094) | BDGP, BDGP EST, BDGP INS | data or information resource, database | Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs. | drosophila genome, cdna, est, transposon insertions, genomic sequencing, gene, FASEB list |
is related to: Bgee: dataBase for Gene Expression Evolution is related to: OpenFlyData.org has parent organization: University of California at Berkeley; Berkeley; USA is parent organization of: Patterns of Gene Expression in Drosophila Embryogenesis |
NHGRI ; NIGMS |
PMID:21177961 | nif-0000-02867, r3d100010624 | http://www.bdgp.org/ | SCR_013094 | 2026-07-28 09:43:10 | 463 | ||||||
|
Bioconductor Resource Report Resource Website 10000+ mentions |
Bioconductor (RRID:SCR_006442) | software repository, software toolkit, software resource | Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. | catalog, analysis, genomic, metadata, comprehension, statistical, data |
lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq |
Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708 |
PMID:15461798 | Free, Freely available | OMICS_01759, nif-0000-10445 | SCR_006442 | 2026-07-28 09:41:34 | 22974 | |||||||
|
riborex Resource Report Resource Website 1+ mentions |
riborex (RRID:SCR_019104) | software toolkit, software resource | Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency. | Ribo-seq data, differential translation, differential translation identification, mapping genome differences, translation efficiency, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA |
NHGRI R01 HG006015 | PMID:28158331 | Free, Available for download, Freely available | biotools:riborex | https://bio.tools/riborex | SCR_019104 | riborex v2.3.4 | 2026-07-28 09:44:51 | 7 | |||||
|
MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software toolkit, software resource | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NSF DEB-2028280; NIAID U19AI110820; NHGRI R01HG005220; NIDDK R24DK110499; NIDDK U54DK102557 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-07-28 09:45:53 | 170 | ||||||||
|
Epiviz Resource Report Resource Website 1+ mentions |
Epiviz (RRID:SCR_022796) | software toolkit, software resource | Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data. | Interactive visual analytics, functional genomics data, interactive visualization tool | is provided by: BICCN | NHGRI R01 HG006102; NHGRI R01 HG005220; Illumina Corporation ; Genentech |
PMID:25086505 | Free, Available for download, Freely available | https://bioconductor.org/packages/epivizr/, https://epiviz.github.io/ | SCR_022796 | 2026-07-28 09:45:43 | 1 | |||||||
|
ataqv Resource Report Resource Website 1+ mentions |
ataqv (RRID:SCR_023112) | software toolkit, software resource | Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments. | QC of ATAC-seq results, visualization of ATAC-seq results, examine aligned reads, mapping quality, | NIDDK R01 DK-117960; American Diabetes Association Pathway to Stop Diabetes ; NHGRI T32 HG00040; NIDDK T32 DK101357; University of Michigan Rackham Predoctoral Fellowship |
PMID:32213349 | Free, Available for download, Freely available | https://parkerlab.github.io/ataqv/demo/ | SCR_023112 | 2026-07-28 09:45:47 | 6 | ||||||||
|
SURVIVOR Resource Report Resource Website 10+ mentions |
SURVIVOR (RRID:SCR_022995) | SURVIVOR | software toolkit, software resource | Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering. | Structural Variant, simulating and evaluating SVs, merging and comparing SVs, reformat or summarize SVs, | Swiss National Science Foundation ; National Science Foundation DBI-1350041; NHGRI R01-HG006677; Wellcome Trust Senior Investigator Award ; Royal Society Wolfson Research Merit Award ; EPSRC Centre for Doctoral Training studentship at UCL CoMPLEX |
PMID:28117401 | Free, Available for download, Freely available | SCR_022995 | StructURal Variant majorIty VOte | 2026-07-28 09:45:50 | 15 | |||||||
|
Merqury Resource Report Resource Website 50+ mentions |
Merqury (RRID:SCR_022964) | software toolkit, software resource | Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers. | reference free quality, completeness, phasing assessment, genome assemblies, quality evaluation based on k-mers | NHGRI | PMID:32928274 | Free, Available for download, Freely available | SCR_022964 | 2026-07-28 09:45:49 | 61 | |||||||||
|
AmpliconArchitect Resource Report Resource Website 10+ mentions |
AmpliconArchitect (RRID:SCR_023150) | software toolkit, software resource | Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers. | call circular DNA, short read WGS data, connected genomic regions identification, simultaneous copy number amplification, amplicon | NIGMS R01GM114362; NHGRI HG010149; NSF NSF-DBI-1458557 |
DOI:10.1038/s41467-018-08200-y | SCR_023150 | 2026-07-28 09:45:52 | 42 | ||||||||||
|
Preprocessing tools for oligonucleotide arrays Resource Report Resource Website 10+ mentions |
Preprocessing tools for oligonucleotide arrays (RRID:SCR_023726) | software toolkit, software resource | Software R package to analyze oligonucleotide arrays at probe level. Supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). Used for annotation of Affymetrix Gene Array data. | analyze oligonucleotide arrays, Affymetrix Gene Array, NimbleGen array, Affymetrix Gene Array data annotation, | Brazilian Funding Agency CAPES ; NCRR R01 RR021967; NHGRI P41 HG004059 |
PMID:20688976 | Free, Available for download, Freely available | SCR_023726 | affycoretools | 2026-07-28 09:45:59 | 13 | ||||||||
|
abSENSE Resource Report Resource Website 1+ mentions |
abSENSE (RRID:SCR_023223) | source code, software resource | Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally. | undetected homolog, gene homolog detection failure, homology search, lineage-specific genes, homology detection failure | Howard Hughes Medical Institute ; NHGRI R01-HG009116; NIGMS RO1-GM43987; NSF 1764269; Simons Center for the Mathematical and Statistical Analysis of Biology 594596; Harvard University |
PMID:33137085 | Free, Available for download, Freely available | http://www.eddylab.org/abSENSE/ | SCR_023223 | 2026-07-28 09:45:53 | 1 | ||||||||
|
SomaticSeq Resource Report Resource Website 1+ mentions |
SomaticSeq (RRID:SCR_024891) | software toolkit, software resource | Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification. | NGS variant calling and classification, somatic mutation detection, somatic mutation calls, single nucleotide variants, detect somatic mutations, | NIGMS R01 GM109836; NHGRI R01 HG007834 |
PMID:26381235 | SCR_024891 | 2026-07-28 09:46:14 | 6 | ||||||||||
|
PEPhub Resource Report Resource Website 1+ mentions |
PEPhub (RRID:SCR_024892) | data or information resource, database, data access protocol, software resource, web service | Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end. | Portable Encapsulated Projects, biological metadata server, sharing, retrieving, validating, sample metadata, | NIGMS R35 GM128636; NHGRI R01 HG012558 |
PMID:37645717 | Free, Available for download, Freely available | https://github.com/pepkit/pephub | SCR_024892 | Portable Encapsulated Projects hub | 2026-07-28 09:46:12 | 2 | |||||||
|
Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software toolkit, software resource | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NIMH R01MH110531; NHGRI R01HG010773; NIMH R01MH116281; NIGMS R01 GM126553; NHGRI R01 HG011883; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-07-28 09:46:14 | 1 | ||||||||
|
Winnowmap Resource Report Resource Website 10+ mentions |
Winnowmap (RRID:SCR_025349) | source code, software resource | Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. | long-read mapping, ONT and PacBio reads, repetitive reference sequences, paralog specific variants within repeats, | NHGRI ; Indian Institute of Science |
PMID:35365778 | Free, Available for download, Freely available | SCR_025349 | Winnowmap2 | 2026-07-28 09:46:20 | 17 | ||||||||
|
pVACtools Resource Report Resource Website 10+ mentions |
pVACtools (RRID:SCR_025435) | software toolkit, software resource | Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design. | Cancer immunotherapy tools, identify and visualize cancer neoantigens, | NCI U01CA209936; NCI U01CA231844; NCI U24CA237719; NHGRI R00HG007940; V Foundation for Cancer Research |
PMID:31907209 | Free, Freely available | SCR_025435 | 2026-07-28 09:46:22 | 27 | |||||||||
|
C3Poa Resource Report Resource Website 1+ mentions |
C3Poa (RRID:SCR_025484) | C3Poa | software application, data analysis software, source code, software resource, data processing software | Software to detect DNA splint sequence raw reads. Computational pipeline for calling consensi on R2C2 nanopore data. | Concatemeric Consensus Caller, Partial Order alignments, detect DNA splint sequence raw reads, calling consensi on R2C2 nanopore data, | NHGRI 1T32HG008345 | PMID:30201725 | Free, Available for download, Freely available, | SCR_025484 | Concatemeric Consensus Caller with Partial Order alignments. | 2026-07-28 09:46:22 | 4 | |||||||
|
Conditional AutoRegressive Deconvolution Resource Report Resource Website 1+ mentions |
Conditional AutoRegressive Deconvolution (RRID:SCR_026310) | CARD | source code, software toolkit, software resource | Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations. | Deconvolution method, spatial transcriptomics, cell-type-specific expression, single-cell RNA sequencing, cell-type composition across tissue locations, | NIGMS R01GM126553; NHGRI R01HG011883; NIGMS R01GM144960 |
PMID:35501392 | Free, Available for download, Freely available | SCR_026310 | , CARD: Conditional AutoRegressive Deconvolution, Conditional autoregressive-based deconvolution | 2026-07-28 09:46:35 | 3 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the kravitz2 Resources search. From here you can search through a compilation of resources used by kravitz2 and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that kravitz2 has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on kravitz2 then you can log in from here to get additional features in kravitz2 such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into kravitz2 you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
