Bioconductor Topics

ATAC-seq Quality Control

Transcription Factor Enrichment Analysis for ATAC-seq

Bias-free Footprint Enrichment Test

Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

Coordinate Covariation Analysis

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Analysis of single-cell epigenomics datasets with a Shiny App

Probabilistic association of DEGs to CREs from differential data

Comparison, Benchmarking & QC of Epigenomic Datasets

find influential TF and Target based on multi-omics data

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

Processing Various Types of Data on GEO and TCGA

Set of 3D genomic interaction analysis tools

MACS: Model-based Analysis for ChIP-Seq

PCAtools: Everything Principal Components Analysis

Replicate oriented Visualization of a genomic region

Set of tools to make V-plots and compute footprint profiles

Differential cell-type-specific allelic imbalance

Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens

Improved ChromVAR (Chromatin Variation Across Regions)

Predict cis-co-accessibility from single-cell chromatin accessibility data

Epigenomic Analysis Package Built for R (epiRomics)

Epigenomic R-based analysis with hidden Markov models

An Easy-to-use Systematic pipeline for ATACseq data analysis

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Proportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Microbiome Data Simulation

Mixture Nested Effects Models

Inferring unobserved perturbations from gene expression data

Generation of null ranges via bootstrapping or covariate matching

POpulation-based Evaluation Metrics

An R package for the creation of complex genomic profile plots

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

scDblFinder

Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions