Showing 6 of total 6 results (show query)
bioc
gscreend:Analysis of pooled genetic screens
Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.
Maintained by Katharina Imkeller. Last updated 5 months ago.
softwarestatisticalmethodpooledscreenscrispr
10.0 match 11 stars 6.34 score 7 scriptsbioc
mnem:Mixture Nested Effects Models
Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.
Maintained by Martin Pirkl. Last updated 4 months ago.
pathwayssystemsbiologynetworkinferencenetworkrnaseqpooledscreenssinglecellcrispratacseqdnaseqgeneexpressioncpp
10.0 match 4 stars 5.64 score 15 scripts 4 dependentsbioc
TAPseq:Targeted scRNA-seq primer design for TAP-seq
Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.
Maintained by Andreas R. Gschwind. Last updated 5 months ago.
singlecellsequencingtechnologycrisprpooledscreens
10.0 match 4 stars 5.38 score 9 scriptsbioc
gCrisprTools:Suite of Functions for Pooled Crispr Screen QC and Analysis
Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.
Maintained by Russell Bainer. Last updated 5 months ago.
immunooncologycrisprpooledscreensexperimentaldesignbiomedicalinformaticscellbiologyfunctionalgenomicspharmacogenomicspharmacogeneticssystemsbiologydifferentialexpressiongenesetenrichmentgeneticsmultiplecomparisonnormalizationpreprocessingqualitycontrolrnaseqregressionsoftwarevisualization
10.0 match 4.78 score 8 scriptsbioc
nempi:Inferring unobserved perturbations from gene expression data
Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.
Maintained by Martin Pirkl. Last updated 5 months ago.
softwaregeneexpressiondifferentialexpressiondifferentialmethylationgenesignalingpathwaysnetworkclassificationneuralnetworknetworkinferenceatacseqdnaseqrnaseqpooledscreenscrisprsinglecellsystemsbiology
10.0 match 2 stars 4.60 score 2 scriptsbioc
pogos:PharmacOGenomics Ontology Support
Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.
Maintained by VJ Carey. Last updated 2 months ago.
pharmacogenomicspooledscreensimmunooncology
10.0 match 4.30 score 10 scripts