spliceJAC: transition genes and state‐specific gene regulation from single‐cell transcriptome data
Extracting dynamical information from single‐cell transcriptomics is a novel task with the
promise to advance our understanding of cell state transition and interactions between …
promise to advance our understanding of cell state transition and interactions between …
SpliceSeq 2.0: A tool for analysis and visualization of splicing variation in RNASeq data
MC Ryan, J Cleland, R Kim, WC Wong… - Europe PMC free … - researchgate.net
Alternative mRNA splicing enables a single gene to produce multiple protein products that
are specific to tissue type or developmental stage. Aberrant splicing patterns lead to …
are specific to tissue type or developmental stage. Aberrant splicing patterns lead to …
PennDiff: detecting differential alternative splicing and transcription by RNA sequencing
Motivation Alternative splicing and alternative transcription are a major mechanism for
generating transcriptome diversity. Differential alternative splicing and transcription (DAST) …
generating transcriptome diversity. Differential alternative splicing and transcription (DAST) …
acorde unravels functionally interpretable networks of isoform co-usage from single cell data
Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to
modulate isoform expression within genes and contribute to cell-type identity. However, the …
modulate isoform expression within genes and contribute to cell-type identity. However, the …
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
Motivation: In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts
and plays an important role in tissue-specific differentiation, and can be misregulated in …
and plays an important role in tissue-specific differentiation, and can be misregulated in …
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples
Motivation As more and larger genomics studies appear, there is a growing need for
comprehensive and queryable cross-study summaries. These enable researchers to …
comprehensive and queryable cross-study summaries. These enable researchers to …
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
I Alqassem, Y Sonthalia, E Klitzke-Feser, H Shim… - …, 2021 - academic.oup.com
Motivation Alternative splicing removes intronic sequences from pre-mRNAs in alternative
ways to produce different forms (isoforms) of mature mRNA. The composition of expressed …
ways to produce different forms (isoforms) of mature mRNA. The composition of expressed …
Leveraging transcript quantification for fast computation of alternative splicing profiles
GP Alamancos, A Pagès, JL Trincado, N Bellora… - Rna, 2015 - rnajournal.cshlp.org
Alternative splicing plays an essential role in many cellular processes and bears major
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …
A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification
Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and
is a key contributor to both normal developmental processes and disease states. While cost …
is a key contributor to both normal developmental processes and disease states. While cost …
Analysis of RNA Transcripts by High‐Throughput RNA Sequencing
For many years, array‐based methods have been used successfully to interrogate the
transcriptome of the cell. These methods rely on quantification of the hybridization intensity …
transcriptome of the cell. These methods rely on quantification of the hybridization intensity …