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bioc
EventPointer:An effective identification of alternative splicing events using junction arrays and RNA-Seq data
EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.
Maintained by Juan A. Ferrer-Bonsoms. Last updated 5 months ago.
alternativesplicingdifferentialsplicingmrnamicroarrayrnaseqtranscriptionsequencingtimecourseimmunooncology
4 stars 6.00 score 6 scriptsbioc
Rhisat2:R Wrapper for HISAT2 Aligner
An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Maintained by Charlotte Soneson. Last updated 3 months ago.
alignmentsequencingsplicedalignmentcpp
4 stars 5.98 score 7 scripts 1 dependentsbioc
CircSeqAlignTk:A toolkit for end-to-end analysis of RNA-seq data for circular genomes
CircSeqAlignTk is designed for end-to-end RNA-Seq data analysis of circular genome sequences, from alignment to visualization. It mainly targets viroids which are composed of 246-401 nt circular RNAs. In addition, CircSeqAlignTk implements a tidy interface to generate synthetic sequencing data that mimic real RNA-Seq data, allowing developers to evaluate the performance of alignment tools and workflows.
Maintained by Jianqiang Sun. Last updated 5 months ago.
sequencingsmallrnaalignmentsoftware
4.30 score 3 scripts