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37 repositories

ProteoSeq
Public
ProteoSeq: Protein Isoform Analysis via Long-read RNA-seq
rna-seq proteomics proteogenomics
rna-seq proteomics proteogenomics long-read-sequencing
Python
•
Other
•0•0•0•1•Updated Apr 14, 2026Apr 14, 2026
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 Apr 10, 2026Apr 10, 2026
espresso
Public
Python
•
Other
•8•64•13•0•Updated Mar 19, 2026Mar 19, 2026
rMATS-long
Public
Python
•
Other
•6•35•7•0•Updated Mar 17, 2026Mar 17, 2026
rmats2sashimiplot
Public
Python
•
GNU General Public License v2.0
•57•160•45•0•Updated Mar 16, 2026Mar 16, 2026
rmats-turbo
Public
C++
•
Other
•63•293•263•2•Updated Mar 4, 2026Mar 4, 2026
NanoTS
Public
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Feb 14, 2026Feb 14, 2026
scCirRL-seq
Public
Haplotype-resolved full-length transcriptome analysis in single cells by scCirRL-seq
single-cell-rna-seq long-read-sequencing allele-specific-splicing
single-cell-rna-seq long-read-sequencing allele-specific-splicing cell-type-specific-splicing
Python
•
MIT License
•1•0•0•0•Updated Dec 3, 2025Dec 3, 2025
IRIS-long
Public
Python
•
Other
•0•0•0•0•Updated Nov 12, 2025Nov 12, 2025
STRIPE
Public
R
•0•0•0•0•Updated Oct 28, 2025Oct 28, 2025
rmats-turbo-tutorial
Public
HTML
•5•6•0•0•Updated Feb 20, 2025Feb 20, 2025
iDARTS
Public
Predicting splicing effects of human genome variants from sequences
Python
•
Other
•0•1•0•0•Updated Nov 20, 2024Nov 20, 2024
IRIS
Public
IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
rna-seq immunotherapy neoantigen
rna-seq immunotherapy neoantigen rna-splicing tumor-antigen
Python
•
Other
•10•29•10•0•Updated Aug 20, 2024Aug 20, 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
tandem-repeats long-reads multiple-sequence-alignment nanopore-sequencing seed-and-chain partial-order-alignment
C
•
MIT License
•2•22•8•0•Updated Jun 17, 2024Jun 17, 2024
DARTS
Public
Deep-learning Augmented RNA-seq analysis of Transcript Splicing
Python
•
Other
•31•115•19•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
simd long-reads multiple-sequence-alignment partial-order-alignment banded-dp consensus-sequence
C
•
MIT License
•3•15•0•0•Updated Jul 20, 2023Jul 20, 2023
lr2rmats
Public
Long read to rMATS
C
•
GNU General Public License v3.0
•6•32•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•12•4•0•Updated Feb 21, 2023Feb 21, 2023
PEGASAS
Public
Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
rna-seq cancer alternative-splicing
rna-seq cancer alternative-splicing signaling-pathways tumor-progression
Python
•11•20•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
expectation-maximization peak-caller iclip peak clip-seq rip-seq eclip
Python
•
GNU General Public License v3.0
•6•32•10•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
•1•3•0•0•Updated Mar 2, 2021Mar 2, 2021
GTEx-brain-sQTL
Public
R
•5•13•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
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

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Xinglab

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All

37 repositories

ProteoSeq

TEQUILA-seq

espresso

rMATS-long

rmats2sashimiplot

rmats-turbo

NanoTS

scCirRL-seq

IRIS-long

STRIPE

rmats-turbo-tutorial

iDARTS

IRIS

TideHunter

DARTS

isoCirc

abPOA

lr2rmats

sparks

PAIRADISE

PEGASAS

SPIRIT

Myc-regulated_AS_PrCa_paper

CLAM

siri

intron-retention-paper

GTEx-brain-sQTL

GLiMMPS

SQUID

ASPRIN

All

All

Repositories list

37 repositories