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 2 months ago
geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncology
4 stars 8.51 score 108 dependencies 1 dependentsmonaLisa - 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 4 days ago
motifannotationvisualizationfeatureextractionepigenetics
36 stars 7.78 score 134 dependencieseisaR - 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 2 months ago
transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
15 stars 7.36 score 32 dependencieseisaR - 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 2 months ago
transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
15 stars 7.36 score 32 dependenciesRbowtie - 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 6 months ago
sequencingalignment
1 stars 6.57 score 0 dependencies 8 dependentsRhisat2 - R Wrapper for HISAT2 Aligner
An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Last updated 6 months ago
alignmentsequencingsplicedalignment
3 stars 5.86 score 96 dependencies 1 dependentssketchR - An R interface for python subsampling/sketching algorithms
Provides an R interface for various subsampling algorithms implemented in python packages. Currently, interfaces to the geosketch and scSampler python packages are implemented. In addition it also provides diagnostic plots to evaluate the subsampling.
Last updated 6 days ago
singlecell
2 stars 4.30 score 56 dependenciesswissknife - 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 5 months ago
8 stars 3.68 score 72 dependencies