alternative-splicing

There are 5 repositories under alternative-splicing topic.

timbitz / Whippet.jl
Lightweight and Fast; RNA-seq quantification at the event-level
alternative-splicing rna-seq
Language:Julia 101
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.
rna-seq-data alternative-splicing scrna-seq-data bioinformatics-pipeline clustering pathway-analysis network-analysis splicing-quantification splicing-visualization python fastq-anaysis bam-files single-cell-splicing cell-cycle cell-type-classification marker-gene-analysis graphical-interface command-line-tool pagerank louvain-community-detection
Language:Python 91
VCCRI / Sierra
Discover differential transcript usage from polyA-captured single cell RNA-seq data
alternative-polyadenylation alternative-splicing isoforms scrna-seq sierra
Language:R 48
huangyh09 / brie
BRIE: Bayesian Regression for Isoform Estimate in Single Cells
alternative-splicing isoform-quantification single-cell rna-seq variantional-inference differential-splicing differential-momentum-gene
Language:Python 40
nf-core / rnasplice
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
nextflow nf-core pipeline workflow alternative-splicing rna rna-seq splicing
Language:Nextflow 34
nuno-agostinho / psichomics
Interactive R package to quantify, analyse and visualise alternative splicing
splicing-quantification data-analyses alternative-splicing tcga differential-splicing-analysis gtex survival bioconductor sra recount2 differential-gene-expression gene-expression rna-seq-data vast-tools
Language:R 33
Xinglab / PEGASAS
Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)
alternative-splicing signaling-pathways rna-seq cancer tumor-progression
Language:Python 18
hclimente / smartas
📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.
manuscript-figures alternative-splicing cancer tcga genomics
Language:Jupyter Notebook 14
Imamachi-n / NGS-Tutorial
NGS Tutorial
rna-seq bric-seq par-clip strand-specific alternative-splicing
Language:HTML 14
Caleydo / vials
Vials is a Caleydo Web application for visualizing alternative splicing based on mRNAseq data.
vials phovea phovera-application alternative-splicing alternative-splicing-analysis d3
Language:TypeScript 13
comprna / ISOTOPE
ISOform-guided prediction of epiTOPEs in cancer
cancer alternative-splicing epitopes-prediction
Language:Python 13
eFP-Seq_Browser
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.
rna-seq rna-seq-mapping bioinformatics webapp data-visualization efp bam arabidopsis alternative-splicing arabidopsis-thaliana database
Language:HTML 12
louadi / NEASE
A network-based approach for exon set enrichment
network-analysis statistics bioinformatics-tool protein-protein-interaction alternative-splicing rna-seq transcriptomics
Language:Python 12
hclimente / spada
⚔️Find splicing-led, functional changes of the proteome.
isoform-switches protein-structure protein-protein-interaction alternative-splicing python
Language:Python 10
PhyloSofS-Team / thoraxe
Use Thor's Axe to cut exons into their evolutionary building blocks :zap:
bioinformatics alternative-splicing protein-evolution exon homology orthology-inference
Language:Python 10
yollct / spycone
Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data
transcriptomics alternative-splicing networks-biology systems-biology time-series isoform-switches
Language:Python 9
dieterich-lab / Baltica
Baltica: integrated differential junction usage
bioinformatics bioinformatics-pipeline alternative-splicing workflows data-integration
Language:R 7
huang-sh / astk
Alternative Splicing ToolKit
as alternative-splicing rna-seq
Language:Python 7
huangyh09 / brie-tutorials
Tutorials for using BRIE
single-cell-rna-seq alternative-splicing rna-velocity differential-splicing differential-momentum-genes variational-inference
Language:Jupyter Notebook 7
shehio / Computational-Biology
computational-biology smith-waterman smith-waterman-alignment gillespie-algorithm gillespie gradient-descent gradient-descent-algorithm gradient-descent-implementation genome-analysis genome-alignment differential-analysis gene-expression alternative-splicing differential-expression differential-expression-analysis single-cell-analysis single-cell-genomics viterbi-algorithm viterbi-decoder bowtie2
Language:Jupyter Notebook 6
areyesq89 / HumanTissuesDEU
Reproducibility of "Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues."
reproducible-research transcriptomics alternative-splicing biostatistics
Language:HTML 4
PhyloSofS-Team / PhyloSofS
A tool to model the evolution and structural impact of alternative splicing
bionformatics alternative-splicing protein-evolution phylogenetic-trees homology-modeling
Language:Python 4
AngryMaciek / snakemake_suppa2
A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.
snakemake-pipeline rna-seq alternative-splicing
Language:Python 3
breecoffey / RNA-Seq-Splicing-Analysis-Pipeline
Computational biology pipeline that quantifies RNA splicing and performs sQTL mapping
bioinformatics-pipeline rna-seq alternative-splicing
Language:Python 3
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
rna-seq-analysis transcriptome quality-check trimming assembly go-annotation alternative-splicing differential-gene-expression
Language:R 3
IsoAligner
JacobHanimann / IsoAligner
IsoAligner: dynamic mapping of amino acid positions across protein isoforms
bioinformatics sequence-alignment sequence-to-sequence amino-acid-sequence aminoacid protein-sequences uniprot-ids refseq ucsc exon-mapping protein-ids needleman-wunsch-algorithm aminoacid-position protein-isoform splice-variants alternative-splicing
Language:Python 3
kdis-lab / SupervisedMethodology
A supervised methodology for analyzing dysregulation in splicing machinery: an application in cancer diagnosis.
transcript-based-analysis alternative-splicing feature-weighting-methods classification-methods explaining-classifier-s-predictions
Language:Python 3
nuno-agostinho / rmats-docker
Docker to run rMATS for splicing quantification and analysis
docker rmats alternative-splicing splicing-quantification
Language:Python 3
UdeS-CoBIUS / SimSpliceEvol
SimSpliceEvol: Alternative splicing-aware simulation of biological sequence evolution
alternative-splicing evolution exon-intron-structure graphical-user-interface simulation transcript-phylogenies transcriptomics
Language:Python 3
yuhuihui2011 / VaSP
Quantification and Visualization of Variations of Splicing in Population
rna-seq alternative-splicing statistics visualization splicing ballgown sqtl 3s-scores
Language:R 3
antoineszatkownik / ASRUs_generator
bioinformatics alternative-splicing
Language:Python 2
SMG5-SMG7
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
bioinformatics rna-seq deseq2 leafcutter isoform-switches alternative-splicing salmon gencode r nmd
Language:R 2
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
bioinformatics rna-seq r deseq2 alternative-splicing salmon gencode nmd isoform-switches leafcutter
Language:R 2
fchen365 / surf
The statistical utility for RBP functions (SURF)
package rna-seq clip-seq integrative-analysis surf differential-analysis alternative-splicing
Language:R 2
KarakulakTulay / CanIsoNet_Web
Functional impact of cancer-specific isoform switching events: Visualization via STRING interaction network
protein-protein-interaction isoform-switches functional-impact alternative-splicing stringdb
Language:HTML 2
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.
alternative-splicing bioinformatics pfam functional-consequences-splicing
Language:R 2

alternative-splicing

timbitz / Whippet.jl

nsalomonis / altanalyze

VCCRI / Sierra

huangyh09 / brie

nf-core / rnasplice

nuno-agostinho / psichomics

Xinglab / PEGASAS

hclimente / smartas

Imamachi-n / NGS-Tutorial

Caleydo / vials

comprna / ISOTOPE

BioAnalyticResource / eFP-Seq_Browser

louadi / NEASE

hclimente / spada

PhyloSofS-Team / thoraxe

yollct / spycone

dieterich-lab / Baltica

huang-sh / astk

huangyh09 / brie-tutorials

shehio / Computational-Biology

areyesq89 / HumanTissuesDEU

PhyloSofS-Team / PhyloSofS

AngryMaciek / snakemake_suppa2

breecoffey / RNA-Seq-Splicing-Analysis-Pipeline

DISC-IISR / RNAseqAnalysis

JacobHanimann / IsoAligner

kdis-lab / SupervisedMethodology

nuno-agostinho / rmats-docker

UdeS-CoBIUS / SimSpliceEvol

yuhuihui2011 / VaSP

antoineszatkownik / ASRUs_generator

boehmv / SMG5-SMG7

boehmv / UPF3

fchen365 / surf

KarakulakTulay / CanIsoNet_Web

rubenchazarra / Transcript-Protein-Domain-Mapper