Biocview "Transcription"

A Framework for visualizing gene set enrichment throughout neurodevelopment

A Functional Approach To Impute Genetically Regulated Expression

alpine

alternative CDF environments (aka probeset mappings)

Analysis for short time-series data

Analysis of alternative splicing using RNA-Seq

Analysis of Alternative Splicing Using RNA-Seq

Analysis of amplicon enrichment panels

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of Large Affymetrix Microarray Data Sets

Analysis of Transposable Elements

AnaLysis routines for ePigenomicS data

Analysis Tools for scATACseq Data with CoGAPS

Analyze Transcription Factor Enrichment

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

An R package estimates the correlations of orthologs and transposable elements between two species

An R package facilitating analysis of RNA modifications, structures, and interactions

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

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

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

An R package to detect chromatin state switches from epigenomic data

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

A package for discriminative motif discovery, designed for high throughput sequencing dataset

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

ArrayAnalysis

A search tool for single cell RNA-seq data by gene lists

A shiny user interface for rTRM

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

Assess Differential Gene Expression Experiments with ERCC Controls

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

A SummarizedExperiment for Ivy-GAP data

A Tidy Transcriptomics introduction to RNA-Seq analyses

A tool for unsupervised projection of single cell RNA-seq data

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Automated functions for comparing various omic data from cbioportal.org

A web interface for gene-set enrichment analyses

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Base NanoString Experiment Class

Bayesian Analysis of Chip-chip experiment

Bayesian Inference of Regulation of Transcriptional Activity

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bias-free Footprint Enrichment Test

Biclustering Analysis and Results Exploration

Big multivariate data plotted interactively

Bioconductor components for general cancer genomics

BioTIP: An R package for characterization of Biological Tipping-Point

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

ceRNAR: An R Package for Identification and Analysis of ceRNAs-miRNA Triplets

Characterization of Alternative Splicing based on Paired-End Reads

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

ChIP-Seq data scaling according to spike-in control

CircRNA transcriptome assembly tool

Classification of alternative splicing and prediction of coding potential from RNA-seq data.

Classify Samples From RNA-Seq Datasets

Clustering of Time Series Gene Expression data

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

Combination Connectivity Mapping

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Comparative Evaluation and Visualization of Differential Expression Analyses

Computational pipeline for computing probability of modification from structure probing experiment data

Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Coordinated Gene Activity in Pattern Sets

CoRegFlux

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Cross omic genetic fingerprinting

Cross Platform Meta-Analysis of Microarray Data

Data-driven Annotation of the Transcriptome

Data for the alpine package vignette

Data Package for the annoFuse Bioconductor Package

Decomposing Heterogeneous Cohorts using Omic Data Profiling

decoupleR: Ensemble of computational methods to infer biological activities from omics data

Delineate outstanding genomic zones of differential gene activity

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Determination of essential phenotypic elements of clusters in high-dimensional entities

dgeAnalysis

Differential Binding of Transcription Factor with ChIP-seq

Differential cell-type-specific allelic imbalance

Differential Co-expression Analysis

Differential Expression Analysis for RNA-seq data through a robust variance component test

Differential gene expression analysis based on the negative binomial distribution

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Differential gene expression data formats converter

Differentially Expressed Gene-Gene pairs

Differentially regulated genes from scRNA-seq data

Discriminant Analysis for Evolutionary Inference

distinct: a method for differential analyses via hierarchical permutation tests

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

DtracePLN: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model

Dynamic Transcriptome Analysis

DynaMO predicts spatiotemporal binding of transcription factors

Empirical Analysis of Digital Gene Expression Data in R

Empirical RNA-seq Sample Size Analysis

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Enrichment Approach to Predict Which Transcription Factors are Regulated

Estimate Promoter Activity from RNA-Seq data

Estimate Systems Immune Response from RNA-seq data

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

EWCE for Multiple Gene Lists

Exon-Intron Split Analysis (EISA) in R

Expression Weighted Celltype Enrichment

Fast Permutation-based Gene Set Analysis

Find Causal Cell-Types Underlying Complex Trait Genetics

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Fit transcriptional regulatory networks using gene expression, priors, machine learning

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

Functional Network Analysis

Functions for analyzing SELEX-seq data

Gene Ontology analyser for RNA-seq and other length biased data

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Generate customized protein databases from NGS data for proteomics search

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Gene regulator enrichment analysis

Gene Set Enrichment Analysis Extended to Contingency Cubes

GeneSet objects from ChIP-Seq experiments

Gene Set Regulation Index

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

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

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

GUI for limma Package with Affymetrix Microarrays

Guitar

Hidden Variable Dynamic Modeling

Higher-Order Deconvolution Survival Analyses

High-Throughput Sequence Analysis using the Aroma Framework

Identification and classification of plant transcription factors

Identification of enriched motif pairs from chromatin interaction data

Identification of genetic Variants affecting Alternative Splicing

Identification of transcriptional regulatory modules from PPI networks

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Identify differential APA usage from RNA-seq alignments

Identifying Differential Effects in Tiling Microarray Data

Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Inference of gene regulatory networks from gene expression data

Inference on agreement between ordered lists

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Integrating Cap Enrichment with Transcript Expression Analysis

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Interactive SummarizedExperiment Explorer

Interactive visualization of scRNA-seq data with Cerebro

Introduction to Tidy Transcriptomics

iSEE Universe

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

Linear model and normality based normalization and transformation method (Linnorm)

Linear Models for Microarray Data

LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates

m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

Make read coverage plots from BigWig files

Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping

Maximum Likelihood Decay Modeling of RNA Degradation Data

Mean Alterations Using Discrete Expression

Minimized Single-Cell Consensus Clustering

miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Monte Carlo Reference-based Consensus Clustering

MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

Multiomic Batch effect Correction

Multiple Beta t-Tests

Multi-Scale Target Explorer

Multivariate Analysis of Transcriptomic Data

NanoString GeoMx Tools

NanoString nCounter Tools

Negative Binomial Beta t-Test

NEUral network-based single-Cell Annotation tool

Outlier Analysis for pairwise differential comparison

Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

PANDA Algorithm

PatchseqMap

Pathway-based data integration of omics data

Pathway fingerprinting for analysis of gene expression arrays

PCAtools: Everything Principal Components Analysis

Perform co-DE gene analysis

PLNet: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model

Predict Combined Function of Transcription Factors

Predicting context-specific m6A regulation of gene expression

Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information

Prediction of pri-miRNA Transcription Start Site

Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Promoter identification from large-scale TSS profiling data

Publication-ready volcano plots with enhanced colouring and labeling

Quality Control of Normalized Gene Expression Data

Quantification of the Tumor Immune contexture from RNA-seq data

Quantitative comparison of multiple ChIP-seq datasets

R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data

RcisTarget: Identify transcription factor binding motifs enriched on a gene list

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

regutools: an R package for data extraction from RegulonDB

R functions for the normalization of Exiqon miRNA array data

RNA-binding protein motif analysis

RNA-Seq multi-mapping Reads Quantification Tool

rnaSeq secondary analyses

RNA-Seq Utilities

R package for analysing TFBSs in DNA sequences

R package for RIVER (RNA-Informed Variant Effect on Regulation)

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for Single-cell RNA-seq Data

scDataviz: single cell dataviz and downstream analyses

scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition

Segvis: A package for visualization of high throughput sequencing data along genomic segments

Shape-based Analysis of Variation in ChIP-seq using Functional PCA

sigFeature: Significant feature selection using SVM-RFE & t-statistic

Single-Cell Consensus Clustering

Single Cell Differential Expression

Single Cell Inference of Regulatory Activity

Single-Cell RNA-Seq Utilities

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Sparse Partial Correlations On Gene Expression

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Splice event prediction and quantification from RNA-seq data

splicegear

Statistical tools for the analysis of ChIP-seq data

Statistical Utility for RBP (RNA binding protein) Functions

Subsampling of high-throughput sequencing count data

Supervised Normalization of Microarrays

Systems EPigenomics Inference of Regulatory Activity

TFregulomeR reveals transcription factors’ context-specific features and functions

The Genomic STate ANnotation Package

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

The tidyomics blog

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

Tool for Evaluation of Cell Identity from Transcription Profiles

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for Managing Seurat Objects

Tools for the Efficient Analysis of High-Resolution Genomics Data

Transcript expression inference and differential expression analysis for RNA-seq data

Transcriptional analysis based on transcriptograms

Transcription Factor High Accumulation Zones

Transcription factor Inference through Gaussian process Reconstruction of Expression

Transcription Factors Association Rules Miner

Transcription Factors Enrichment Analysis

Transcriptome-guided quality assessment of m6A-seq data

Transcript Quantification Import with Automatic Metadata

Translational control assessment from ribosome footprint and total RNA libraries

tricycle: Transferable Representation and Inference of cell cycle

TSS sequencing data analysis

Unified methods for the inference and analysis of gene regulatory networks

Unified Statistical Modeling of Omics Data

Unlocking iSEE for transcript-level visualization

Very simple high level analysis of Affymetrix data

Visualise microarray and RNAseq data using gene ontology annotations

What the Package Does TODOELI

Biocview "Transcription"

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