SkeletalVis - Exploration and Visualisation of Skeletal Transcriptomics Data
Allows search and visualisation of a collection of uniformly processed skeletal transcriptomic datasets. Includes methods to identify datasets where genes of interest are differentially expressed and find datasets with a similar gene expression pattern to a query dataset Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM (2019) <doi:10.1093/bioinformatics/bty947>.
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gene-expressionosteoarthritis
3.70 score 305 downloadsperturbMatch - Match Transcriptomics Signatures to Single-Gene Perturbation References
Matches a query transcriptomics signature against a reference database of single-gene perturbation signatures, ranking the perturbations whose expression response most resembles the query and so nominating the regulators most likely to drive the observed change. Query signatures derived from a differential expression result are scored using cosine, GSEA and signed-Jaccard similarity metrics. Reference databases are supplied as HDF5-backed SummarizedExperiment objects for memory-efficient handling of large perturbation collections, and helper functions rank and visualise the best-matching regulators.
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generegulationtranscriptomicstranscriptiongenesetenrichmentgenetargetgeneexpressiondifferentialexpression
3.30 score 4 scriptsperturbMatchData - Reference Perturbation Signatures from GEO RNA-seq Experiments
Provides the reference perturbation expression signatures used by the perturbMatch package, which ranks the single-gene perturbations whose expression response most resembles a query signature. Each reference signature summarises the differential expression observed after a single-gene perturbation (knockdown, knockout or overexpression) in a human RNA-seq experiment deposited in the Gene Expression Omnibus. Signatures are summarised either by the characteristic direction method or by limma, each with and without surrogate variable analysis batch correction, giving four datasets served as HDF5-backed SummarizedExperiment objects.
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experimenthubexperimentdataexpressiondatarnaseqdatasequencingdatahomo_sapiens_datageo
2.70 score