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 30 days ago
geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncologycurlbzip2xz-utilszlibcpp
8.59 score 5 stars 1 dependents 74 scripts 712 downloadsmonaLisa - 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 9 days ago
motifannotationvisualizationfeatureextractionepigenetics
8.06 score 40 stars 53 scripts 322 downloadseisaR - 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 5 days ago
transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
7.52 score 15 stars 63 scriptseisaR - 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 30 days ago
transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
7.52 score 15 stars 63 scripts 298 downloadsRbowtie - 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 30 days ago
sequencingalignment
6.80 score 1 stars 8 dependents 22 scripts 835 downloadsRhisat2 - 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 2 months ago
alignmentsequencingsplicedalignmentcpp
6.08 score 4 stars 1 dependents 7 scripts 482 downloadssketchR - 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 2 months ago
singlecell
5.41 score 2 stars 3 scripts 160 downloadsswissknife - 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 30 days ago
cpp
3.89 score 8 stars 12 scripts