ChIPQC - Quality metrics for ChIPseq data
Quality metrics for ChIPseq data.
Last updated 4 months ago
sequencingchipseqqualitycontrolreportwriting
2.83 score 158 dependenciesHerper - The Herper package is a simple toolset to install and manage conda packages and environments from R
Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.
Last updated 4 months ago
infrastructuresoftware
5 stars 1.31 score 13 dependenciesprofileplyr - Visualization and annotation of read signal over genomic ranges with profileplyr
Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.
Last updated 4 months ago
chipseqdataimportsequencingchiponchipcoverage
0.71 score 203 dependenciesbasecallQC - Working with Illumina Basecalling and Demultiplexing input and output files
The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
Last updated 4 months ago
sequencinginfrastructuredataimportqualitycontrol
0.71 score 116 dependenciesRfastp - An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).
Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.
Last updated 4 months ago
qualitycontrolsequencingpreprocessingsoftware
0.09 score 36 dependenciestracktables - Build IGV tracks and HTML reports
Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.
Last updated 4 months ago
sequencingreportwriting
0.09 score 47 dependencies