timbitz/Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level

Language: Julia - Size: 21.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 112 - Forks: 22

BioAnalyticResource/eFP-Seq_Browser

An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.

Language: HTML - Size: 78.8 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 13 - Forks: 7

SalomonisLab/altanalyze3

AltAnalyze version 3 is a Python3 library to integrate and compare diverse RNA isoform datasets.

Language: Python - Size: 14 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 4 - Forks: 3

PhyloSofS-Team/thoraxe

Use Thor's Axe to cut exons into their evolutionary building blocks :zap:

Language: Python - Size: 9.3 MB - Last synced at: 24 days ago - Pushed at: 25 days ago - Stars: 12 - Forks: 3

shiquan/Yano

An R package to perform Spatial dissimilarity analysis in single cells

Language: C - Size: 6.34 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

dieterich-lab/Baltica

Baltica: integrated differential junction usage

Language: R - Size: 57.6 MB - Last synced at: 29 days ago - Pushed at: about 2 years ago - Stars: 10 - Forks: 3

nf-core/rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Language: Nextflow - Size: 160 MB - Last synced at: 12 days ago - Pushed at: 13 days ago - Stars: 54 - Forks: 31

nuno-agostinho/psichomics

Interactive R package to quantify, analyse and visualise alternative splicing

Language: R - Size: 59.1 MB - Last synced at: about 16 hours ago - Pushed at: about 18 hours ago - Stars: 37 - Forks: 11

zhou-lei5/MRAS

Language: R - Size: 67.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

daisybio/NEASE

A network-based approach for exon set enrichment

Language: Python - Size: 49.3 MB - Last synced at: 9 days ago - Pushed at: about 2 months ago - Stars: 14 - Forks: 2

nsalomonis/altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

Language: Python - Size: 264 MB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 103 - Forks: 31

VCCRI/Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data

Language: R - Size: 19.9 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 50 - Forks: 17

estepi/SpliceNet

Scripts associated to transcriptome-wide analysis of the effects of systematic knock down of splicing factors and regulators using siRNAs in HeLa cells

Language: R - Size: 8.1 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 0

huang-sh/astk

Alternative Splicing ToolKit

Language: Python - Size: 103 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 9 - Forks: 0

Imamachi-n/NGS-Tutorial

NGS Tutorial

Language: HTML - Size: 626 KB - Last synced at: about 2 months ago - Pushed at: about 8 years ago - Stars: 15 - Forks: 7

WanluLiuLab/yasim

Language: Python - Size: 2.5 MB - Last synced at: 28 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

lasseignelab/230926_EJ_Setbp1_AlternativeSplicing

This repository is for our 2024 manuscript, Cell-type-specific alternative splicing in the cerebral cortex of a Schinzel-Giedion Syndrome patient variant mouse model

Language: R - Size: 84.4 MB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

yollct/spycone

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

Language: Python - Size: 93.9 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 0

SoniaRuiz/introverse_v2

IntroVerse 2.0 Update

Language: R - Size: 890 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

lasseignelab/230227_EJ_MouseBrainIsoDiv

This repository is the current repository for our Jones et al. 2024 manuscript titled Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage.

Language: R - Size: 53.7 MB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

UdeS-CoBIUS/SimSpliceEvol

SimSpliceEvol: Alternative splicing-aware simulation of biological sequence evolution

Language: Python - Size: 51.9 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 2

huangyh09/brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells

Language: Python - Size: 1.72 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 40 - Forks: 15

simon-bt/sm-rnaseq-splicing

Snakemake pipeline for alternative slicing analysis with VAST-TOOLS

Language: Python - Size: 17.6 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

TheOrangeBraincell/DetectSpliceVariant

Repository for method to analyse the relationship between germline variants and somatic mutations and alternative splicing in breast cancer patients based on RNA-Seq data,

Language: Python - Size: 390 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

alexaburchak/BreastCancer_Genomics

Analysis of RNA-Seq data for approximately 3500 breast tumors from the SCAN-B project to investigate differential splicing patterns between molecular subtypes and clinical phenotypes

Language: R - Size: 24.1 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

jdutel42/Project_2

Language: Shell - Size: 10.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

Semillas/SemillasClient

Mobile App Social Currency and Geolocated Marketplace

Language: JavaScript - Size: 3.06 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 1

Caleydo/vials 📦

Vials is a Caleydo Web application for visualizing alternative splicing based on mRNAseq data.

Language: TypeScript - Size: 544 KB - Last synced at: 5 months ago - Pushed at: over 7 years ago - Stars: 13 - Forks: 4

TheOrangeBraincell/variants_in_AS_Pipeline

Depository for Bioinformatics Master Project HT2022-VT2023

Language: Python - Size: 943 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

Xinglab/PEGASAS

Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)

Language: Python - Size: 54.8 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 18 - Forks: 11

hclimente/spada

⚔️Find splicing-led, functional changes of the proteome.

Language: Python - Size: 158 MB - Last synced at: 20 days ago - Pushed at: almost 6 years ago - Stars: 10 - Forks: 1

PhyloSofS-Team/PhyloSofS

A tool to model the evolution and structural impact of alternative splicing

Language: Python - Size: 1.54 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 0

ashleymaeconard/time2splice

Method to identify temporal and sex-specific alternative splicing from multi-omic data, specifically RNA-seq + (CUT&RUN or ChIP-seq).

Language: Shell - Size: 15 MB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

UdeS-CoBIUS/TranscriptOrthology

Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach

Language: Python - Size: 16.4 MB - Last synced at: 27 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

comprna/ISOTOPE

ISOform-guided prediction of epiTOPEs in cancer

Language: Python - Size: 1.22 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 6

DISC-IISR/RNAseqAnalysis

The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction

Language: R - Size: 126 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

yuhuihui2011/VaSP

Quantification and Visualization of Variations of Splicing in Population

Language: R - Size: 8.98 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0

Ibrahim-Olajide/ibrahim-olajide.github.io

Variation in Gene caused by Mutation and Alternative Splicing: Identification and Characterization of Pathogenic Variants in TRY, OCA2, HPS-1 and OA1 Genes that leads to Albinism

Size: 762 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

kdis-lab/SupervisedMethodology

A supervised methodology for analyzing dysregulation in splicing machinery: an application in cancer diagnosis.

Language: Python - Size: 856 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

kdis-lab/IMIBIC-projects

This repository contains all the studies made in colaboration with IMIBIC

Language: HTML - Size: 447 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

huangyh09/diceseq

Dynamic Isoform spliCing Estimator via sequencing data

Language: Python - Size: 2.86 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 1

boehmv/UPF3

Code and scripts for the RNA-seq analysis of project: Deciphering the cellular roles and dissecting functional regions of UPF3A and UPF3B in human NMD

Language: R - Size: 5.29 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

SoniaRuiz/introverse

A database of introns and alternative splicing events across human tissues

Language: HTML - Size: 1.28 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

areyesq89/HumanTissuesDEU

Reproducibility of "Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues."

Language: HTML - Size: 6.69 MB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 3

shehio/Computational-Biology

Language: Jupyter Notebook - Size: 21.6 MB - Last synced at: 7 months ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 1

AngryMaciek/snakemake_vast_tools 📦

My personal snakemake pipeline for VAST-TOOLS execution

Language: Python - Size: 61.5 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

AngryMaciek/snakemake_suppa2 📦

A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.

Language: Python - Size: 2.89 MB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 1

JacobHanimann/IsoAligner

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

Language: Python - Size: 215 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 2

hclimente/smartas

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Language: Jupyter Notebook - Size: 504 MB - Last synced at: 3 months ago - Pushed at: about 7 years ago - Stars: 14 - Forks: 5

boehmv/SMG5-SMG7

Code and scripts for the RNA-seq analysis of project: SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity

Language: R - Size: 2.98 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

huangyh09/brie-tutorials

Tutorials for using BRIE

Language: Jupyter Notebook - Size: 37.6 MB - Last synced at: 11 days ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 0

Caleydo/vials_server 📦

Reading Genomic Files and provide data as API

Language: Python - Size: 88.9 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 1

zaharsm/pricingtable-css3

pricing page customized using css3

Language: CSS - Size: 641 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

rubenchazarra/Transcript-Protein-Domain-Mapper

Method for retrieving and visualising the protein domains of any protein coding isoform and of different genomes. Enables joint visualisations representing alternative splicing events.

Language: R - Size: 656 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

KarakulakTulay/CanIsoNet_Web

Functional impact of cancer-specific isoform switching events: Visualization via STRING interaction network

Language: HTML - Size: 161 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 2

federicomarini/trend-db

Home to the development of the TREND-DB application

Language: R - Size: 68 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 0 - Forks: 2

mtp-usz/IsoAligner Fork of JacobHanimann/IsoAligner

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

Language: Python - Size: 215 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

nuno-agostinho/vast-tools-docker

Docker to run VAST-TOOLS for splicing quantification and analysis

Language: Dockerfile - Size: 1.3 MB - Last synced at: 9 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

nuno-agostinho/suppa-docker

Docker to run SUPPA for splicing quantification and analysis

Language: Python - Size: 1.23 MB - Last synced at: 9 days ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 1

nuno-agostinho/miso-docker

Docker to run MISO for splicing quantification and analysis

Language: Python - Size: 5.07 MB - Last synced at: 9 days ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 3

nuno-agostinho/whippet-docker

Docker to run Whippet for splicing quantification and analysis

Size: 1000 Bytes - Last synced at: 9 days ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

nuno-agostinho/rmats-docker

Docker to run rMATS for splicing quantification and analysis

Language: Python - Size: 23.5 MB - Last synced at: 9 days ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 4

antoineszatkownik/ASRUs_generator

Language: Python - Size: 24.3 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

nuno-agostinho/alternativeSplicingEvents

Alternative splicing annotation for AnnotationHub

Language: R - Size: 12.7 KB - Last synced at: 9 days ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

nuno-agostinho/alternativeSplicingEvents.hg19

Alternative splicing event annotation for Human assembly (hg19)

Language: R - Size: 20.7 MB - Last synced at: 9 days ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

helmutcarter/bioinformatics_utilities

Language: Python - Size: 23.4 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

breecoffey/RNA-Seq-Splicing-Analysis-Pipeline

Computational biology pipeline that quantifies RNA splicing and performs sQTL mapping

Language: Python - Size: 105 MB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 3

nuno-agostinho/alternativeSplicingEvents.hg38

Alternative splicing event annotation for Human assembly (hg38)

Language: R - Size: 20.7 MB - Last synced at: 9 days ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

erpl-iiserb/Hypoxia

Language: R - Size: 7.48 MB - Last synced at: 11 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

kdis-lab/LSTM-rank-isoforms

Performing Cancer Diagnosis via an Isoform Level Expression Ranking-based LSTM Model

Language: Python - Size: 13.7 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1