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.
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motifannotationvisualizationfeatureextractionepigenetics
8.12 score 49 stars 127 scripts 836 downloadsQuasR - 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.
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geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncologycurlbzip2xz-utilszlibcpp
8.01 score 7 stars 97 scripts 903 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.
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transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
7.47 score 18 stars 82 scripts 622 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.
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sequencingalignment
6.96 score 1 stars 7 dependents 32 scripts 834 downloadsTabulaMurisSenisData - Bulk and single-cell RNA-seq data from the Tabula Muris Senis project
This package provides access to RNA-seq data generated by the Tabula Muris Senis project via the Bioconductor project. The data is made available without restrictions by the Chan Zuckerberg Biohub. It is provided here without further processing, collected in the form of SingleCellExperiment objects.
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singlecelldataexperimentdatarnaseqdataexperimenthubdatapkg
6.13 score 4 stars 45 scriptsRhisat2 - 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.
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alignmentsequencingsplicedalignmentcpp
5.91 score 3 stars 1 dependents 12 scripts 573 downloadsmutscan - Preprocessing and Analysis of Deep Mutational Scanning Data
Provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.
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geneticvariabilitygenomicvariationpreprocessingzlibcppopenmp
5.89 score 14 stars 14 scripts 280 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.
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singlecell
5.38 score 3 stars 9 scripts 326 downloadsorthosData - Data for the orthos package
`orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.
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experimentdatarnaseqdataexperimenthubdatapkg
4.48 score 1 dependents 1 scriptsorthos - `orthos` is an R package for variance decomposition using conditional variational auto-encoders
`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.
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rnaseqdifferentialexpressiongeneexpression
3.95 score 3 stars 5 scripts 378 downloads