esATAC - An Easy-to-use Systematic pipeline for ATACseq data analysis
This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.
Last updated 24 days ago
immunooncologysequencingdnaseqqualitycontrolalignmentpreprocessingcoverageatacseqdnaseseqatac-seqbioconductorpipeline
6.11 score 23 stars 3 scripts 222 downloadsRbowtie2 - An R Wrapper for Bowtie2 and AdapterRemoval
This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging. The package contains wrapper functions that allow for genome indexing and alignment to those indexes. The package also allows for the creation of .bam files via Rsamtools.
Last updated 24 days ago
sequencingalignmentpreprocessing
5.39 score 3 packages 27 scripts 638 downloadspipeFrame - Pipeline framework for bioinformatics in R
pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.
Last updated 24 days ago
softwareinfrastructureworkflowstep
4.08 score 1 stars 1 packages 2 scripts 252 downloads