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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.
Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming.
Proper citation: Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) Copy
https://www.bioconductor.org/packages/release/bioc/html/SingleR.html
Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently.
Proper citation: SingleR (RRID:SCR_023120) Copy
https://psbweb05.psb.ugent.be/conet/microbialnetworks/spieceasi.php
Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets.
Proper citation: Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) Copy
https://benjjneb.github.io/dada2/
Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.
Proper citation: DADA2 (RRID:SCR_023519) Copy
https://github.com/cliu32/athlates
Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms.
Proper citation: ATHLATES (RRID:SCR_023689) Copy
https://github.com/mwang87/MassQueryLanguage
Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data.
Proper citation: MassQL (RRID:SCR_025106) Copy
https://github.com/sxf296/drug_targeting
Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules.
Proper citation: drug perturbation Gene Set Enrichment Analysis (RRID:SCR_025351) Copy
https://github.com/immunogenomics/masc
Software tool for testing whether specified covariate influences membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation.
Proper citation: Mixed effects association testing for single cells (RRID:SCR_025632) Copy
https://github.com/dviraran/xCell
Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis.
Proper citation: xCell (RRID:SCR_026446) Copy
https://github.com/GreenleafLab/chromVAR
Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data.
Proper citation: chromvar (RRID:SCR_026570) Copy
https://github.com/RGLab/CytoML
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.
Proper citation: CytoML (RRID:SCR_027485) Copy
https://github.com/VincentGardeux/demuxlet?tab=readme-ov-file
Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq.
Proper citation: demuxlet (RRID:SCR_027855) Copy
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