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bioc
ATACseqQC:ATAC-seq Quality Control
ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencingdnaseqatacseqgeneregulationqualitycontrolcoveragenucleosomepositioningimmunooncology
7.12 score 146 scripts 1 dependentsbioc
psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.
Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.
sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-toolscpp
36 stars 6.95 score 31 scripts
sritchie73
NetRep:Permutation Testing Network Module Preservation Across Datasets
Functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing; Ritchie et al. (2015) <doi: 10.1016/j.cels.2016.06.012>.
Maintained by Scott Ritchie. Last updated 4 years ago.
12 stars 6.84 score 16 scripts 3 dependentsbioc
CAGEr:Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.
Maintained by Charles Plessy. Last updated 5 months ago.
preprocessingsequencingnormalizationfunctionalgenomicstranscriptiongeneexpressionclusteringvisualization
6.12 score 73 scriptsbioc
rexposome:Exposome exploration and outcome data analysis
Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.
Maintained by Xavier Escribà Montagut. Last updated 5 months ago.
softwarebiologicalquestioninfrastructuredataimportdatarepresentationbiomedicalinformaticsexperimentaldesignmultiplecomparisonclassificationclustering
5.70 score 28 scripts 1 dependentsbioc
InTAD:Search for correlation between epigenetic signals and gene expression in TADs
The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.
Maintained by Konstantin Okonechnikov. Last updated 5 months ago.
epigeneticssequencingchipseqrnaseqhicgeneexpressionimmunooncology
4.30 score 6 scriptsbioc
codelink:Manipulation of Codelink microarray data
This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.
Maintained by Diego Diez. Last updated 5 months ago.
microarrayonechanneldataimportpreprocessing
4.20 score 5 scriptsbioc
MIRit:Integrate microRNA and gene expression to decipher pathway complexity
MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.
Maintained by Jacopo Ronchi. Last updated 13 days ago.
softwaregeneregulationnetworkenrichmentnetworkinferenceepigeneticsfunctionalgenomicssystemsbiologynetworkpathwaysgeneexpressiondifferentialexpressionmirnamirna-mrna-interactionmirna-seqmirnaseq-analysiscpp
1 stars 4.18 score 2 scripts