Xinglab

All

33 repositories

rmats2sashimiplot
Public
Python
•
GNU General Public License v2.0
•56•137•30•0•Updated Jan 30, 2025Jan 30, 2025
TEQUILA-seq
Public
The scripts contained in this repository were used for processing, analyzing, and visualizing TEQUILA-seq data.
Python
•
Other
•0•8•1•0•Updated Jan 23, 2025Jan 23, 2025
rMATS-long
Public
Python
•
Other
•2•26•3•0•Updated Dec 10, 2024Dec 10, 2024
iDARTS
Public
Predicting splicing effects of human genome variants from sequences
Python
•
Other
•0•1•0•0•Updated Nov 20, 2024Nov 20, 2024
rmats-turbo
Public
C++
•
Other
•54•237•200•2•Updated Nov 19, 2024Nov 19, 2024
ProteoSeq
Public
ProteoSeq: A proteogenomics workflow leveraging long-read RNA-seq data for discovery of isoform-level peptides and proteins.
rna-seq proteomics proteogenomics long-read-sequencing
Python
•
Other
•0•0•0•0•Updated Nov 18, 2024Nov 18, 2024
IRIS
Public
IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
rna-seq immunotherapy neoantigen tumor-antigen rna-splicing
Python
•
Other
•9•24•10•0•Updated Aug 20, 2024Aug 20, 2024
espresso
Public
Python
•
Other
•4•58•10•0•Updated Aug 5, 2024Aug 5, 2024
TideHunter
Public
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
tandem-repeats long-reads multiple-sequence-alignment nanopore-sequencing seed-and-chain partial-order-alignment
C
•
MIT License
•2•20•8•0•Updated Jun 17, 2024Jun 17, 2024
DARTS
Public
Deep-learning Augmented RNA-seq analysis of Transcript Splicing
Python
•
Other
•32•111•18•0•Updated Feb 7, 2024Feb 7, 2024
isoCirc
Public
isoCirc
Python
•
GNU General Public License v3.0
•4•10•5•0•Updated Nov 27, 2023Nov 27, 2023
abPOA
Public
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
simd long-reads multiple-sequence-alignment partial-order-alignment banded-dp consensus-sequence
C
•
MIT License
•3•13•0•0•Updated Jul 20, 2023Jul 20, 2023
rmats-turbo-tutorial
Public
HTML
•4•3•0•0•Updated May 12, 2023May 12, 2023
lr2rmats
Public
Long read to rMATS
C
•
GNU General Public License v3.0
•6•31•3•0•Updated May 5, 2023May 5, 2023
sparks
Public
R
•0•0•0•0•Updated Apr 19, 2023Apr 19, 2023
PAIRADISE
Public
Paired Replicate Analysis of Allelic Differential Splicing Events
Python
•4•11•3•0•Updated Feb 21, 2023Feb 21, 2023
PEGASAS
Public
Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
rna-seq cancer alternative-splicing signaling-pathways tumor-progression
Python
•11•18•1•0•Updated Jun 16, 2022Jun 16, 2022
SPIRIT
Public
Perl
•0•0•0•0•Updated Apr 11, 2022Apr 11, 2022
Myc-regulated_AS_PrCa_paper
Public
Scripts for plotting figures and running analysis throughout the manuscript
R
•4•11•0•0•Updated Nov 2, 2021Nov 2, 2021
CLAM
Public
CLIP-seq Analysis of Multi-mapped reads
expectation-maximization peak-caller iclip peak clip-seq rip-seq eclip
Python
•
GNU General Public License v3.0
•6•29•5•0•Updated Jul 20, 2021Jul 20, 2021
siri
Public
Python
•1•5•0•0•Updated Jun 8, 2021Jun 8, 2021
intron-retention-paper
Public
Jupyter Notebook
•
MIT License
•2•3•0•0•Updated Mar 2, 2021Mar 2, 2021
GTEx-brain-sQTL
Public
R
•5•12•0•0•Updated Jun 2, 2020Jun 2, 2020
GLiMMPS
Public
GLiMMPS
R
•1•6•0•1•Updated Oct 8, 2019Oct 8, 2019
SQUID
Public
Stringent Quantitation of Unspliced Intron by Deep-sequencing
rna-seq intron-retention intron-pi
Python
•
GNU General Public License v3.0
•2•2•0•0•Updated Sep 16, 2019Sep 16, 2019
ASPRIN
Public
Python
•
GNU General Public License v3.0
•1•3•0•0•Updated Jul 24, 2019Jul 24, 2019
rMATS-DVR
Public
Python
•
GNU General Public License v3.0
•13•18•3•0•Updated Jan 17, 2019Jan 17, 2019
SURVIV
Public
Survival Analysis of mRNA Isoform Variation
Python
•
Other
•7•6•1•0•Updated Oct 31, 2018Oct 31, 2018
Xinglab.github.io
Public
HTML
•0•1•0•0•Updated Sep 27, 2018Sep 27, 2018
SEASTAR
Public
SEASTAR - Systematic Evaluation of Alternative transcription STArt site in RNA
Python
•
GNU General Public License v3.0
•5•13•2•0•Updated Jan 21, 2018Jan 21, 2018