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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ped-sim Resource Report Resource Website 1+ mentions |
ped-sim (RRID:SCR_026957) | software resource, simulation software, source code, software application | Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances. | Pedigree simulator, simulate pedigree structures, simulating relatives, sex-specific, sex averaged, genetic maps, | NIGMS R35 GM133805; Alfred P. Sloan Research Fellowship ; United States-Israel Binational Science Foundation ; NHLBI R01 HL0113323; NHLBI P01 HL045222; NIDDK R01 DK047482; NIDDK R01 DK053889; NIGMS T32 GM007617; NIGMS T32 GM083937; Wellcome Trust |
PMID:31860654 | Free, Available for download, Freely available | SCR_026957 | Ped-sim | 2026-02-14 02:09:22 | 2 | ||||||||
|
BEERS2 Resource Report Resource Website |
BEERS2 (RRID:SCR_027287) | software resource, simulation software, source code, software application | Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. | RNA-seq reads, simulation of RNA-seq reads, | NCATS 5UL1TR000003; NHLBI R01HL155934; NHLBI R01HL147472; NIGMS DP2GM146251 |
PMID:38605641 | Free, Available for download, Freely available | SCR_027287 | 2026-02-14 02:09:19 | 0 | |||||||||
|
CytoML Resource Report Resource Website 1+ mentions |
CytoML (RRID:SCR_027485) | software resource, source code, software toolkit | Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. | Cross-platform cytometry data sharing, cross-platform import, export, sharing, gated cytometry data, import gated cytometry data, | NIGMS R01 GM118417; Bill and Melinda Gates Foundation ; NIAID UM1 AI068635 |
PMID:30551257 | Free, Available for download, Freely available | https://www.bioconductor.org/packages/release/bioc/html/CytoML.html | SCR_027485 | 2026-02-14 02:10:03 | 5 | ||||||||
|
BioLiP Resource Report Resource Website 100+ mentions |
BioLiP (RRID:SCR_027685) | data or information resource, database | Semi-manually curated database for biologically relevant ligand-protein binding interactions. Structure data are collected primarily from Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. Database used for serving needs of ligand-protein docking, virtual ligand screening and protein function annotation.BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes, integrates structural alignment algorithms with structure prediction techniques, which enables composite protein structure and sequence-based searching. | curated database, ligand-protein binding interactions, ligand-protein docking, virtual ligand screening, protein function annotation, | uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) | National Science Foundation ; NIGMS GM083107; NIGMS GM084222 |
PMID:23087378 PMID:37522378 |
Free, Freely available | SCR_027685 | BioLiP2 | 2026-02-14 02:09:59 | 115 | |||||||
|
SQuIRE Resource Report Resource Website 10+ mentions |
SQuIRE (RRID:SCR_027719) | SQuIRE | software resource, source code, software toolkit | Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression. | RNA-seq analysis, quantitative and locus-specific picture of TE expression, Transposable Elements expression, | NIGMS R01GM124531; NIGMS P50GM107632 |
PMID:30624635 | Free, Available for download, Freely available | SCR_027719 | , Software for Quantifying Interspersed Repeat Expression (SQuIRE), Software for Quantifying Interspersed Repeat Expression | 2026-02-14 02:09:36 | 10 |
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