recoup - An R package for the creation of complex genomic profile plots

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

Last updated 4 months ago

immunooncologysoftwaregeneexpressionpreprocessingqualitycontrolrnaseqchipseqsequencingcoverageatacseqchiponchipalignmentdataimport

1 stars 1.45 score 116 dependencies

metaseqR2 - An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Last updated 4 months ago

softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq

1.38 score 227 dependencies

sitadela - An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.

Last updated 4 months ago

softwareworkflowsteprnaseqtranscriptionsequencingtranscriptomicsbiomedicalinformaticsfunctionalgenomicssystemsbiologyalternativesplicingdataimportchipseq

0.71 score 93 dependencies