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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | alignment software, data processing software, image analysis software, software application, software resource | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-09-05 06:28:02 | 2 | |||||||
|
AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | alignment software, data processing software, image analysis software, software application, software resource, source code | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI R01 HG2362; NSF CCF0347992; NSF EF 03-31494 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-09-05 06:28:01 | 400 | ||||
|
fermi-lite Resource Report Resource Website 1+ mentions |
fermi-lite (RRID:SCR_016112) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource, standalone software | Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling. | assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, calling | is related to: Illumina | NHGRI U54 HG003037; NIGMS GM100233 |
PMID:26220959 | Free, Available for download | SCR_016112 | FermiKit, Fml-asm | 2026-09-05 06:28:03 | 4 | |||||||
|
ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | American Society of Hematology Scholar Award ; Defense Advanced Research Project Agency ; International Collaborative Award ; NCI R35 CA209919; NCI U2C CA233311; NHGRI RM1 HG007735; NHGRI UM1 HG009436; NHGRI UM1 HG009442; NIAID U19 AI057266; NIA K99 AG059918; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR, https://www.archrproject.com/, https://github.com/GreenleafLab/ArchR_2020 | SCR_020982 | 2026-09-05 06:29:32 | 424 | ||||||||
|
AbundantOTU+ Resource Report Resource Website 1+ mentions |
AbundantOTU+ (RRID:SCR_016527) | AbundantOTU | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset. | pyrosequencing, 16S, rRNA, gene, operational, taxonomic, unit, abundant, species, dataset |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
NHGRI R01 HG004908; NHLBI U01 HL09896001 |
PMID:22102981 | Free, Available for download, Freely available | SCR_016527 | AbundantOTU:Abundant Operational Taxonomic Unit, Abundant OTU, AbundantOTU+ | 2026-09-05 06:28:10 | 1 | ||||||
|
LINCS Project Resource Report Resource Website 50+ mentions |
LINCS Project (RRID:SCR_016486) | LINCS | consortium, data or information resource, database, organization portal, portal, project portal | Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center. | data integration, network biology, gene expression, L1000, MCF10A, MEMA, P100, LINCS program, LINCS project, systems biology, systems pharmacology, FASEB list |
is related to: Drug Gene Budger is related to: LINCS Joint Project - Breast Cancer Network Browser is related to: piNET |
cancer, heart disease, neurodegenerative disorder | NHGRI U54 HG008097; NHGRI U54 HG008098; NHGRI U54 HG008100; NHLBI U54 HL127365; NHLBI U54 HL127366; NHLBI U54 HL127624; NIH Common Fund ; NINDS U54 NS091046 |
PMID:29199020 | Free, Freely available | SCR_016487 | SCR_016486 | LINCS, Library of Integrated Network based Cellular Signatures, LINCS Program | 2026-09-05 06:28:09 | 56 | ||||
|
MR-PRESSO Resource Report Resource Website 100+ mentions |
MR-PRESSO (RRID:SCR_023697) | software resource, software toolkit | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | American Heart Association Cardiovascular Genome Phenome Discovery ; AstraZeneca ; Goldfinch Bio ; NHGRI 5U01 HG009088; NHLBI R01 HL139865; NIGMS R35 GM124836; NIMH 1R01 MH094469; NIMH 1R01 MH107649 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-09-05 06:33:15 | 100 | ||||||||
|
Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
Austrian Science Fund J-3401; Dutch Brain Foundation ; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NHGRI F32HG007805; NHGRI HG007022; NHGRI R01 HG006399; NHLBI HL117626; NIMH R01 MH101244; NWO 480-05-003; Wellcome Trust WT098051 |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-09-05 06:33:00 | 57 | |||||
|
Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | data analytics software, software application, software resource | Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. | Genome distance estimation, metagenome distance estimation, MinHash, mutation distance, sequence, sequence set |
is listed by: Debian is listed by: OMICtools |
NHGRI ; NIH |
PMID:27323842 | Free, Available for download, Freely available | OMICS_10468 | https://mash.readthedocs.io/en/latest/, https://sources.debian.org/src/mash/ | SCR_019135 | 2026-09-05 06:33:05 | 75 | ||||||
|
rtracklayer Resource Report Resource Website 10+ mentions |
rtracklayer (RRID:SCR_021325) | software resource, software toolkit | Software R package for interfacing with genome browsers.Supports integration of existing genome browsers with experimental data analyses performed in R. R interface to genome annotation files and UCSC genome browser. | Existing genome browsers integration, genome annotation files interface, interfacing with genome browsers | NHGRI P41 HG004059 | PMID:19468054 | Free, Available for download, Freely available | https://github.com/lawremi/rtracklayer | SCR_021325 | 2026-09-05 06:33:07 | 22 | ||||||||
|
Adaptive Shrinkage in R Resource Report Resource Website 10+ mentions |
Adaptive Shrinkage in R (RRID:SCR_023486) | ashr | software resource, software toolkit | Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation. | adaptive shrinkage, large scale hypothesis testing, false discovery rate estimation, | Gordon and Betty Moore Foundation ; NHGRI HG02585 |
PMID:27756721 | Free, Available for download, Freely available | SCR_023486 | 2026-09-05 06:33:14 | 10 | ||||||||
|
CHISEL Resource Report Resource Website 1+ mentions |
CHISEL (RRID:SCR_023220) | CHISEL | software application, software resource | Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers. | infer allele and haplotype specific copy numbers, individual cells, low coverage single cell DNA sequencing data, weak allelic signals, weak signals integration, | Chan Zuckerberg Initiative DAF grants ; NCI P30CA072720; NCI U24CA211000; NHGRI R01HG007069; NSF CCF 1053753; O’Brien Family Fund for Health Research ; Wilke Family Fund for Innovation |
DOI:10.1038/s41587-020-0661-6 | Free, Available for download, Freely available | SCR_023220 | Copy-number Haplotype Inference in Single-cell by Evolutionary Links | 2026-09-05 06:33:13 | 3 | |||||||
|
zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NHGRI HG006431; NIDA DA14546; NIGMS GM63904 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-09-05 06:32:38 | 4 | ||||
|
HiCDCPlus Resource Report Resource Website 1+ mentions |
HiCDCPlus (RRID:SCR_025317) | software resource, software toolkit | Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP | Hi-C/HiChIP interaction calling, differential analysis, statistical analysis of Hi-C and HiChIP data sets, systematic 3D interaction calls, | NHGRI U01 HG009395; NIDDK U01 DK128852 |
PMID:34099725 | Free, Available for download, Freely available | https://bitbucket.org/leslielab/hicdcplus/src/master/ | SCR_025317 | , HiC-DC+, Hi-C Direct Caller Plus, HiCDCPlus (HiC-DC+) | 2026-09-05 06:34:55 | 1 | |||||||
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longshot Resource Report Resource Website 1+ mentions |
longshot (RRID:SCR_025318) | software resource, source code | Software variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). Enables accurate variant calling in diploid genomes from single-molecule long read sequencing. Takes as input aligned BAM/CRAM file and outputs phased VCF file with variants and haplotype information. | variant calling, diploid genomes, long error prone reads, single molecule long read sequencing, | NHGRI R01 HG010149 | DOI:10.1038/s41467-019-12493-y | Free, Available for download, Freely available | SCR_025318 | 2026-09-05 06:34:55 | 6 | |||||||||
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tRNA Analysis of eXpression Resource Report Resource Website 1+ mentions |
tRNA Analysis of eXpression (RRID:SCR_025486) | tRAX | data analysis software, data processing software, software application, software resource | Software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data. Used for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications. | tRNA-derived small RNAs, mature tRNAs, inference of RNA modifications, high-throughput small RNA sequencing data, | has parent organization: University of California at Santa Cruz; California; USA | NHGRI R01HG006753 | DOI:10.1101/2022.07.02.498565 PMID:26214130 |
Free, Available for download, Freely available, | SCR_025486 | tRNA Analysis of eXpression (tRAX) | 2026-09-05 06:34:59 | 3 | ||||||
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glmpca Resource Report Resource Website 1+ mentions |
glmpca (RRID:SCR_025517) | software resource, software toolkit, source code | Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data. | dimension reduction, non-normally distributed data, principal components analysis, | Chan-Zuckerberg Initiative ; NCI T32CA009337; NHGRI P41HG004059; NHGRI R00HG009007; NHGRI R01HG005220; NIGMS R01GM083084 |
PMID:31870412 | Free, Available for download, Freely available, | https://CRAN.R-project.org/package=glmpca | SCR_025517 | generalized version of principal components analysis | 2026-09-05 06:35:00 | 2 | |||||||
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WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software resource, software toolkit, source code | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG006123; NHGRI HG007036; NIGMS GM007197; NIMH MH101825; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-09-05 06:35:00 | 3 | |||||||||
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PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software resource, software toolkit | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | American Society of Hematology ; Howard Hughes Medical Institute ; NHGRI RM1 HG007735; NIGMS R35 GM128636 |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-09-05 06:34:41 | 2 | ||||||||
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Single Cell Pathway Analysis Resource Report Resource Website 1+ mentions |
Single Cell Pathway Analysis (RRID:SCR_024909) | SCPA | data analysis software, data processing software, software application, software resource, source code | Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes. | pathway analysis, scRNA-seq data analysis, single cell RNA-seq data, | Intramural Research Program of the NIH ; National Heart ; Lung ; and Blood Institute ; NHGRI R01 HG006137 |
PMID:36417885 | Free, Available for download, Freely available | https://github.com/jackbibby1/SCPA/ | SCR_024909 | Single Cell Pathway Analysis (SCPA) | 2026-09-05 06:34:44 | 3 |
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