QuasR - Quantify and Annotate Short Reads in R

This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.

Last updated 24 days ago

geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncology

8.46 score 4 stars 1 packages 80 scripts 678 downloads

monaLisa - Binned Motif Enrichment Analysis and Visualization

Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of the obtained results are also provided.

Last updated 24 days ago

motifannotationvisualizationfeatureextractionepigenetics

7.88 score 37 stars 49 scripts 302 downloads

eisaR - Exon-Intron Split Analysis (EISA) in R

Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

Last updated 24 days ago

transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq

7.45 score 15 stars 63 scripts 298 downloads

Rbowtie - R bowtie wrapper

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.

Last updated 24 days ago

sequencingalignment

6.57 score 1 stars 8 packages 22 scripts 835 downloads

swissknife - Handy code shared in the FMI CompBio group

A collection of useful R functions performing various tasks that might be re-usable and worth sharing.

Last updated 19 days ago

3.89 score 8 stars 12 scripts