methylKit - DNA methylation analysis from high-throughput bisulfite sequencing results
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
Last updated 4 months ago
dnamethylationsequencingmethylseq
201 stars 7.40 score 96 dependencies 3 dependentsgenomation - Summary, annotation and visualization of genomic data
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
Last updated 4 months ago
annotationsequencingvisualizationcpgisland
72 stars 4.80 score 96 dependencies 5 dependentsmergen - AI-Driven Code Generation, Explanation and Execution for Data Analysis
Employing artificial intelligence to convert data analysis questions into executable code, explanations, and algorithms. The self-correction feature ensures the generated code is optimized for performance and accuracy. 'mergen' features a user-friendly chat interface, enabling users to interact with the AI agent and extract valuable insights from their data effortlessly.
Last updated 2 months ago
10 stars 2.28 score 35 dependencies 1 dependents