BRIE: Bayesian Regression for Isoform Estimate in Single Cells
Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.
Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu
Nanopore 3' end-capture sequencing (Begik et al., Nat Methods 2022)
A pipeline for processing single-cell and spatial long-read transcriptomic data
long read differential expression analysis and splice variant analysis
A Snakemake pipeline developed to quantify isoforms expression levels in large RNA-seq datasets and find poly-A sites
Joint modeling of multiple RNA-seq samples for accurate isoform quantification
Comparing translation of open reading frames within individual transcripts
An awesome alternative-splicing pipeline that runs leafcutter and IsoformSwitchAnalyzeR.
RNA-seq workflow: gene-level exploratory analysis and differential expression.
Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function
simple R-shiny app to visualize frequncies of isoforms within single genes for different hematopoietic cell lines
Docker to run sailfish for quantification of isoform abundance
A Snakemake pipeline developed to quantify isoforms expression levels in large RNA-seq datasets and find poly-A sites
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