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bioc
epigraHMM:Epigenomic R-based analysis with hidden Markov models
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.
Maintained by Pedro Baldoni. Last updated 5 months ago.
chipseqatacseqdnaseseqhiddenmarkovmodelepigeneticszlibopenblascppopenmp
4.94 score 88 scriptsbioc
NADfinder:Call wide peaks for sequencing data
Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencingdnaseqgeneregulationpeakdetection
4.18 score 1 scripts
henrikbengtsson
aroma.cn:Copy-Number Analysis of Large Microarray Data Sets
Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
proprietaryplatformsacghcopynumbervariantssnpmicroarrayonechanneltwochanneldataimportdatarepresentationpreprocessingqualitycontrol
1 stars 2.70 score 9 scripts