bamsignals - Extract read count signals from bam files
This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.
Last updated 5 months ago
dataimportsequencingcoveragealignment
12 stars 8.93 score 19 dependencies 12 dependentsnormr - Normalization and difference calling in ChIP-seq data
Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.
Last updated 5 months ago
bayesiandifferentialpeakcallingclassificationdataimportchipseqripseqfunctionalgenomicsgeneticsmultiplecomparisonnormalizationpeakdetectionpreprocessingalignment
11 stars 5.93 score 81 dependencies