Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "AlternativeSplicing" keyword
maser 1.20.0
Mapping Alternative Splicing Events to pRoteins3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 16 stars on GitHub - 1 maintainer
factR 1.4.0
Functional Annotation of Custom Transcriptomes3 versions - Latest release: 6 months ago - 1.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...3 versions - Latest release: 6 months ago - 28.3 thousand downloads total - 1 maintainer
Ularcirc 1.20.0
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)3 versions - Latest release: 6 months ago - 6.51 thousand downloads total - 1 maintainer
IntEREst 1.26.0
Intron-Exon Retention Estimator3 versions - Latest release: 6 months ago - 11 thousand downloads total - 2 maintainers
FLAMES 1.8.0
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data3 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
DRIMSeq 1.30.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq3 versions - Latest release: 6 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
PAIRADISE 1.18.0
PAIRADISE: Paired analysis of differential isoform expression3 versions - Latest release: 6 months ago - 7.24 thousand downloads total - 2 maintainers
proActiv 1.12.0
Estimate Promoter Activity from RNA-Seq data3 versions - Latest release: 6 months ago - 4.46 thousand downloads total - 44 stars on GitHub - 1 maintainer
VarCon 1.10.0
VarCon: an R package for retrieving neighboring nucleotides of an SNV3 versions - Latest release: 6 months ago - 2.8 thousand downloads total - 1 maintainer
ASpli 2.12.0
Analysis of Alternative Splicing Using RNA-Seq3 versions - Latest release: 6 months ago - 1 dependent package - 17 thousand downloads total - 1 maintainer
customProDB 1.42.1
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics ...4 versions - Latest release: 2 months ago - 26 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...3 versions - Latest release: 6 months ago - 7.55 thousand downloads total - 1 maintainer
RgnTX 1.4.0
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and am...3 versions - Latest release: 6 months ago - 1.6 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 42.5 thousand downloads total - 1 maintainer
SGSeq 1.36.0
Splice event prediction and quantification from RNA-seq data3 versions - Latest release: 6 months ago - 3 dependent packages - 42.5 thousand downloads total - 1 maintainer
wiggleplotr 1.26.0
Make read coverage plots from BigWig files3 versions - Latest release: 6 months ago - 1 dependent package - 14.7 thousand downloads total - 1 maintainer
IMAS 1.26.0
Integrative analysis of Multi-omics data for Alternative Splicing3 versions - Latest release: 6 months ago - 9.74 thousand downloads total - 1 maintainer
VaSP 1.14.0
Quantification and Visualization of Variations of Splicing in Population3 versions - Latest release: 6 months ago - 3.14 thousand downloads total - 3 stars on GitHub - 1 maintainer
MBttest 1.30.0
Multiple Beta t-Tests3 versions - Latest release: 6 months ago - 9.63 thousand downloads total - 1 maintainer
kissDE 1.22.0
Retrieves Condition-Specific Variants in RNA-Seq Data3 versions - Latest release: 6 months ago - 8.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
TIN 1.34.0
Transcriptome instability analysis3 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 1 maintainer
pfamAnalyzeR 1.2.0
Identification of domain isotypes in pfam data3 versions - Latest release: 6 months ago - 1 dependent package - 4.36 thousand downloads total - 1 stars on GitHub - 1 maintainer
metaseqR2 1.14.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...3 versions - Latest release: 6 months ago - 5.12 thousand downloads total - 1 maintainer
SpliceWiz 1.4.1
interactive analysis and visualization of alternative splicing in R4 versions - Latest release: 4 months ago - 2.6 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.1 thousand downloads total - 1 maintainer
SplicingGraphs 1.42.0
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them3 versions - Latest release: 6 months ago - 28.1 thousand downloads total - 1 maintainer
GSReg 1.36.0
Gene Set Regulation (GS-Reg)3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 2 maintainers
SplicingFactory 1.10.0
Splicing Diversity Analysis for Transcriptome Data3 versions - Latest release: 6 months ago - 2.68 thousand downloads total - 3 stars on GitHub - 1 maintainer
GeneStructureTools 1.22.0
Tools for spliced gene structure manipulation and analysis3 versions - Latest release: 6 months ago - 9.35 thousand downloads total - 1 maintainer
IVAS 2.22.0
Identification of genetic Variants affecting Alternative Splicing3 versions - Latest release: 6 months ago - 1 dependent package - 14.4 thousand downloads total - 1 maintainer
pairedGSEA 1.2.0
Paired DGE and DGS analysis for gene set enrichment analysis3 versions - Latest release: 6 months ago - 1.13 thousand downloads total - 2 stars on GitHub - 1 maintainer
IsoBayes 1.2.0
IsoBayes: Single Isoform protein inference Method via Bayesian Analyses3 versions - Latest release: 16 days ago - 832 downloads total - 5 stars on GitHub - 1 maintainer
regsplice 1.30.0
L1-regularization based methods for detection of differential splicing4 versions - Latest release: 6 days ago - 9.76 thousand downloads total - 3 stars on GitHub - 1 maintainer
sitadela 1.12.0
An R package for the easy provision of simple but complete tab-delimited genomic annotation from ...3 versions - Latest release: 10 days ago - 2.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
4 versions - Latest release: 20 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data4 versions - Latest release: 20 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 20 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 20 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
BANDITS 1.20.0
BANDITS: Bayesian ANalysis of DIfferenTial Splicing4 versions - Latest release: 10 days ago - 1 dependent package - 7.51 thousand downloads total - 17 stars on GitHub - 1 maintainer
GenomicPlot 1.2.0
Plot profiles of next generation sequencing data in genomic features9 versions - Latest release: 11 days ago - 1.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
3 versions - Latest release: 14 days ago - 10 dependent packages - 234 thousand downloads total - 1 maintainer
DEXSeq 1.50.0
Inference of differential exon usage in RNA-Seq3 versions - Latest release: 14 days ago - 10 dependent packages - 234 thousand downloads total - 1 maintainer
FRASER 2.0.0
Find RAre Splicing Events in RNA-Seq Data4 versions - Latest release: 21 days ago - 8 thousand downloads total - 13 stars on GitHub - 1 maintainer
InterMineR 1.26.0
R Interface with InterMine-Powered Databases4 versions - Latest release: 13 days ago - 10.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
3 versions - Latest release: 14 days ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
puma 3.46.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...3 versions - Latest release: 14 days ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
OutSplice 1.4.0
Comparison of Splicing Events between Tumor and Normal Samples3 versions - Latest release: 14 days ago - 1.13 thousand downloads total - 1 stars on GitHub - 1 maintainer
fishpond 2.10.0
Fishpond: downstream methods and tools for expression data3 versions - Latest release: 14 days ago - 1 dependent package - 27.1 thousand downloads total - 21 stars on GitHub - 1 maintainer
NxtIRFcore 1.6.0 removed
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using ...1 version - Latest release: 7 months ago - 1.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
psichomics 1.30.0
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation4 versions - Latest release: 16 days ago - 14.4 thousand downloads total - 33 stars on GitHub - 1 maintainer
saseR 1.0.0
Scalable Aberrant Splicing and Expression Retrieval1 version - Latest release: 22 days ago - 179 downloads total - 0 stars on GitHub - 1 maintainer
ModCon 1.10.0
Modifying splice site usage by changing the mRNP code, while maintaining the genetic code2 versions - Latest release: 6 months ago - 2.39 thousand downloads total - 1 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
EventPointer 3.10.0
An effective identification of alternative splicing events using junction arrays and RNA-Seq data2 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
SPLINTER 1.28.0
Splice Interpreter of Transcripts2 versions - Latest release: 6 months ago - 9.93 thousand downloads total - 0 stars on GitHub - 1 maintainer
erccdashboard 1.36.0
Assess Differential Gene Expression Experiments with ERCC Controls2 versions - Latest release: 6 months ago - 18.7 thousand downloads total - 7 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: 7 months ago - 3.82 thousand downloads total - 1 stars on GitHub - 1 maintainer
dasper 1.9.0 removed
Detecting abberant splicing events from RNA-sequencing data1 version - Latest release: 7 months ago - 1 dependent package - 2.76 thousand downloads total - 14 stars on GitHub - 1 maintainer
alpine 1.26.0 removed
alpine1 version - Latest release: 7 months ago - 12.2 thousand downloads total - 1 maintainer
NBSplice 1.18.0 removed
Negative Binomial Models to detect Differential Splicing1 version - Latest release: 7 months ago - 5.1 thousand downloads total - 1 maintainer
Related Keywords
Software
55
RNASeq
43
DifferentialSplicing
35
GeneExpression
32
Sequencing
31
DifferentialExpression
27
Transcription
26
ImmunoOncology
25
Visualization
16
Transcriptomics
16
Coverage
13
MultipleComparison
13
FunctionalGenomics
12
Regression
10
Genetics
10
GeneSetEnrichment
9
BatchEffect
9
DataImport
9
SystemsBiology
8
Bayesian
8
Normalization
8
BiomedicalInformatics
8
Microarray
8
TimeCourse
7
Clustering
7
StatisticalMethod
7
Preprocessing
7
QualityControl
7
GeneRegulation
6
Pathways
6
ExonArray
6
mRNAMicroarray
6
Annotation
6
ChIPSeq
5
Proteomics
5
FunctionalPrediction
5
SNP
5
Epigenetics
5
TwoChannel
4
ProprietaryPlatforms
4
OneChannel
4
CellBiology
4
GenePrediction
3
genomics
3
MicroRNAArray
3
KEGG
3
WorkflowStep
3
rna-seq
3
TranscriptomeVariant
3
splicing
3
SingleCell
3
r
3
bioconductor
2
ExperimentalDesign
2
alternative-splicing
2
Survival
2
statistics
2
gene-expression
2
transcriptomics
2
GUI
2
SAGE
2
Reactome
2
rna-seq-data
2
GenomeAnnotation
2
Alignment
2
MassSpectrometry
2
DataRepresentation
2
diagnostics
2
DifferentialMethylation
2
rna-seq-analysis
2
Network
2
Metabolomics
2
Cheminformatics
2
VariantAnnotation
1
intermine
1
ChipOnChip
1
HTA2.0
1
biology
1
GenomeWideAssociation
1
GO
1
rare-disease
1
NetworkInference
1
GraphAndNetwork
1
vast-tools
1
tcga
1
survival
1
sra
1
splicing-quantification
1
recount2
1
gtex
1
differential-splicing-analysis
1
differential-gene-expression
1
data-analyses
1
PrincipalComponent
1
scrnaseq
1
salmon
1
rnaseq
1
LongRead
1
alternative-promoters
1
promoter-activity
1