Biocview "Transcription"

A Framework for visualizing gene set enrichment throughout neurodevelopment
A Framework for visualizing gene set enrichment throughout neurodevelopment
A functional approach to impute Genetically Regulated Expression
A functional approach to impute Genetically Regulated Expression
alpine
alpine
alpine
alternative CDF environments (aka probeset mappings)
alternative CDF environments (aka probeset mappings)
Analysis for short time-series data
Analysis for short time-series data
Analysis for short time-series data
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of amplicon enrichment panels
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 CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
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 Cap Analysis of Gene Expression (CAGE) data using Bioconductor
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
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 discriminative motif discovery, designed for high throughput sequencing dataset
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
A shiny user interface for rTRM
A shiny user interface for rTRM
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
A SummarizedExperiment for Ivy-GAP data
A SummarizedExperiment for Ivy-GAP data
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
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)
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
A web interface for gene-set enrichment analyses
A web interface for gene-set enrichment analyses
Bayesian Analysis of Chip-chip experiment
Bayesian Analysis of Chip-chip experiment
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
Biclustering Analysis and Results Exploration
Biclustering Analysis and Results Exploration
Big multivariate data plotted interactively
Bioconductor components for general cancer genomics
Bioconductor components for general cancer genomics
Characterization of Alternative Splicing based on Paired-End Reads
Characterization of Alternative Splicing based on Paired-End Reads
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPexoQual
ChIPexoQual
ChIP-Seq data scaling according to spike-in control
ChIP-Seq data scaling according to spike-in control
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Combination Connectivity Mapping
Combination Connectivity Mapping
Combination Connectivity Mapping
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
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
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Cross omic genetic fingerprinting
Cross omic genetic fingerprinting
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Data for the alpine package vignette
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Differential Binding of Transcription Factor with ChIP-seq
Differential Binding of Transcription Factor with ChIP-seq
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential gene expression data formats converter
Differential gene expression data formats converter
Dynamic Transcriptome Analysis
Dynamic Transcriptome Analysis
DynaMO predicts spatiotemporal binding of transcription factors
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Empirical RNA-seq Sample Size Analysis
Empirical RNA-seq Sample Size Analysis
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functions for analyzing SELEX-seq data
Functions for analyzing SELEX-seq data
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased 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 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
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Enrichment Analysis Extended to Contingency Cubes
GeneSet objects from ChIP-Seq experiments
Gene Set Regulation Index
Gene Set Regulation Index
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
GUI for limma package with Affymetrix microarrays
GUI for limma Package with Affymetrix Microarrays
Guitar
Guitar
Hidden Variable Dynamic Modeling
Hidden Variable Dynamic Modeling
High-Throughput Sequence Analysis using the Aroma Framework
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of transcriptional regulatory modules from PPI networks
Identification of transcriptional regulatory modules from PPI networks
Identify differential APA usage from RNA-seq alignments
Identify differential APA usage from RNA-seq alignments
Identify differential APA usage from RNA-seq alignments
Identifying Differential Effects in Tiling Microarray Data
Identifying Differential Effects in Tiling Microarray Data
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Inference on agreement between ordered lists
Inference on agreement between ordered lists
Inference on agreement between ordered lists
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Integrating Cap Enrichment with Transcript Expression Analysis
Integrating Cap Enrichment with Transcript Expression Analysis
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Joint analysis of multiple ChIP-Seq data sets
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Linear Models for Microarray Data
Linear Models for Microarray Data
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
MAGMA.Celltyping
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping
Mapping protein-DNA interactions in highly repetitive regions of the genomes with prior-enhanced read mapping
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Monte Carlo Reference-based Consensus Clustering
Monte Carlo Reference-based Consensus Clustering
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
Multi-Omics Data Fusion for Cancer Module Discovery
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple Beta t-Tests
Multivariate Analysis of Transcriptomic Data
Multivariate Analysis of Transcriptomic Data
Multivariate Analysis of Transcriptomic Data
Multivariate Analysis of Transcriptomic Data
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PatchseqMap
Pathway-based data integration of omics data
Pathway-based data integration of omics data
Pathway-based data integration of omics data
Pathway-based data integration of omics data
Pathway fingerprinting for analysis of gene expression arrays
Pathway fingerprinting for analysis of gene expression arrays
Pathway fingerprinting for analysis of gene expression arrays
Prediction of pri-miRNA Transcription Start Site
Prediction of pri-miRNA Transcription Start Site
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Promoter identification from large-scale TSS profiling data
Publication-ready volcano plots with enhanced colouring and labeling
Publication-ready volcano plots with enhanced colouring and labeling
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantitative comparison of multiple ChIP-seq datasets
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
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
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 gene list
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
R functions for the normalization of Exiqon miRNA array data
R functions for the normalization of Exiqon miRNA array data
RNA-binding protein motif analysis
RNA-binding protein motif analysis
RNA-Seq multi-mapping Reads Quantification Tool
rnaSeq secondary analyses
rnaSeq secondary analyses
RNA-Seq Utilities
RNA-Seq Utilities
RNA-Seq Utilities
R package for analysing TFBSs in DNA sequences
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
Segvis: A package for visualization of high throughput sequencing data along genomic segments
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
sigFeature: Significant feature selection using SVM-RFE & t-statistic
sigFeature: Significant feature selection using SVM-RFE & t-statistic
Single-Cell Clustering Visualization
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Differential Expression
Single-Cell RNA-Seq Utilities
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
Splice event prediction and quantification from RNA-seq data
Splice event prediction and quantification from RNA-seq data
Splice event prediction and quantification from RNA-seq data
splicegear
splicegear
Statistical tools for the analysis of ChIP-seq data
Statistical tools for the analysis of ChIP-seq data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Systems EPigenomics Inference of Regulatory Activity
Systems EPigenomics Inference of Regulatory Activity
The Genomic STate ANnotation Package
The Genomic STate ANnotation Package
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Tool for Evaluation of Cell Identity from Transcription Profiles
Tool for Evaluation of Cell Identity from Transcription Profiles
Transcript expression inference and differential expression analysis for RNA-seq data
Transcript expression inference and differential expression analysis for RNA-seq data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcription Factor High Accumulation Zones
Transcription Factor High Accumulation Zones
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcription Factors Association Rules Miner
Transcription Factors Association Rules Miner
Transcription Factors Association Rules Miner
Transcriptome-guided quality assessment of m6A-seq data
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
Translational control assessment from ribosome footprint and total RNA libraries
Very simple high level analysis of Affymetrix data
Very simple high level analysis of Affymetrix data
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations