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bioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
8 stars 12.08 score 1.8k scripts 49 dependentsbioc
SpliceWiz:interactive analysis and visualization of alternative splicing in R
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
Maintained by Alex Chit Hei Wong. Last updated 17 days ago.
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
16 stars 6.41 score 8 scripts
tingtingzhan
ThomasJeffersonUniv:Handy Tools for TJU/TJUH Employees
Functions for admin needs of employees of Thomas Jefferson University and Thomas Jefferson University Hospital, Philadelphia, PA.
Maintained by Tingting Zhan. Last updated 18 days ago.
3.45 score
pjumppanen
BuildSys:System for Building and Debugging C/C++ Dynamic Libraries
A build system based on 'GNU make' that creates and maintains (simply) make files in an R session and provides GUI debugging support through 'Microsoft Visual Code'.
Maintained by Paavo Jumppanen. Last updated 4 years ago.
2 stars 2.30 score 1 scripts