ExpressionAtlas - Download datasets from EMBL-EBI Expression Atlas
This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.
Last updated 5 months ago
expressiondataexperimentdatasequencingdatamicroarraydataarrayexpress
4.35 score 60 dependenciesCexoR - An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.
Last updated 5 months ago
functionalgenomicssequencingcoveragechipseqpeakdetection
4.00 score 98 dependenciesfCCAC - functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomics, as it allows both to evaluate reproducibility of replicates, and to compare different datasets to identify potential correlations. fCCAC applies functional Canonical Correlation Analysis to allow the assessment of: (i) reproducibility of biological or technical replicates, analyzing their shared covariance in higher order components; and (ii) the associations between different datasets. fCCAC represents a more sophisticated approach that complements Pearson correlation of genomic coverage.
Last updated 5 months ago
epigeneticstranscriptionsequencingcoveragechipseqfunctionalgenomicsrnaseqatacseqmnaseseq
4.00 score 124 dependencies