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IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.
geneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicingvisualizationstatisticalmethodtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologytranscriptomicsrnaseqannotationfunctionalpredictiongenepredictiondataimportmultiplecomparisonbatcheffectimmunooncology
108 stars 9.26 score 125 scriptsbioc
RIVER:R package for RIVER (RNA-Informed Variant Effect on Regulation)
An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.
Maintained by Yungil Kim. Last updated 5 months ago.
geneexpressiongeneticvariabilitysnptranscriptionfunctionalpredictiongeneregulationgenomicvariationbiomedicalinformaticsfunctionalgenomicsgeneticssystemsbiologytranscriptomicsbayesianclusteringtranscriptomevariantregressionfunctional-variantsvariant
11 stars 5.52 score 5 scriptsbioc
SplicingFactory:Splicing Diversity Analysis for Transcriptome Data
The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.
Maintained by Endre Sebestyen. Last updated 5 months ago.
transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgini-indexrna-seqshannon-entropysimpson-indexsplicing
4 stars 5.20 score 1 scriptsbioc
airpart:Differential cell-type-specific allelic imbalance
Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.
Maintained by Wancen Mu. Last updated 5 months ago.
singlecellrnaseqatacseqchipseqsequencinggeneregulationgeneexpressiontranscriptiontranscriptomevariantcellbiologyfunctionalgenomicsdifferentialexpressiongraphandnetworkregressionclusteringqualitycontrol
2 stars 4.78 score 2 scriptsbioc
transmogR:Modify a set of reference sequences using a set of variants
transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.
Maintained by Stevie Pederson. Last updated 13 days ago.
alignmentgenomicvariationsequencingtranscriptomevariantvariantannotationzlib
4.74 score 2 scriptsbioc
pfamAnalyzeR:Identification of domain isotypes in pfam data
Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.
Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.
alternativesplicingtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologyannotationfunctionalpredictiongenepredictiondataimport
1 stars 3.78 score 1 scripts 1 dependents