… SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinfor…
BRIE: transcriptome-wide splicing quantification in single cells. Genome Biol 2017;18:123. …

… RNA-seq with single cells or single cell nuclei RNA is … expressed isoforms with differentially
spliced sites can enhance … will not capture transcriptome-wide patterns that represent activity …

… We used both the output files for two different purposes: (1) to detect the inter-tumor
heterogeneity we extracted FPKM normalized isoform estimates from the BRIE output for different …

… analyze splicing dynamics at single-cell resolution. Here, we present MARVEL, a comprehensive
R package for single-cell splicing analysis … For BRIE, differential splicing analysis was …

… The following settings were used to quantify splicing with BRIE: exons have to be located
on autosomes and input chromosomes and should not be overlapped by any other …

… Genomic coordinates corresponding to alternative splicing events can be extracted from the
splicing detection and quantitation tools such as BRIE and MISO [12, 16]. VALERIE supports …

… However, BRIE requires performing a pairwise comparison between every two … a single
cell dataset from CRC patients. Thus, systematic evaluation of differential splicing across T cells …

… method for single cells, isoform quantification could be used … To mimic actual cell-wise and
gene-wise read depth from … gene from one healthy human PBMC donor [Single Cell Gene …

… Since, with a few exceptions 60,61 , splicing analysis tools rarely integrate functional
information, we annotated the long read-defined transcripts using IsoAnnotLite (https://isoannot.…

… transcriptome-wide view on the isoform usage changes. In Figure 1C, we perform a DTU
analysis … the great potential of differential splicing analysis for these data largely unexploited. In …