psichomics - Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.
Last updated 25 days ago
sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-tools
7.11 score 35 stars 31 scripts 216 downloadscTRAP - Identification of candidate causal perturbations from differential gene expression data
Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.
Last updated 25 days ago
differentialexpressiongeneexpressionrnaseqtranscriptomicspathwaysimmunooncologygenesetenrichmentbioconductorbioinformaticscmapgene-expressionl1000
5.08 score 5 stars 16 scripts 170 downloads