R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

sirusb/R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Bioconductor-mirror/R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Bioconductor-mirror/BAGS

A Bayesian Approach for Geneset Selection

BAGS

A Bayesian Approach for Geneset Selection

pcaMethods

A collection of PCA methods

Bioconductor-mirror/pcaMethods

A collection of PCA methods

wevanjohnson/ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor-mirror/ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

compbiomed/ASSIGN

Adaptive Signature Selection and InteGratioN (ASSIGN)

Bioconductor-mirror/ALDEx2

Analysis Of Differential Abundance Taking Sample Variation Into Account

ggloor/ALDEx_bioc

Analysis Of Differential Abundance Taking Sample Variation Into Account

ALDEx2

Analysis Of Differential Abundance Taking Sample Variation Into Account

azhu513/apeglm

Approximate posterior estimation for GLM coefficients

apeglm

Approximate posterior estimation for GLM coefficients

databio/RPIM

Assess epigenetic heterogeneity with proportion of intermediate methylation

databio/epihet

Assess epigenetic heterogeneity with proportion of intermediate methylation

snaketron/genphen

A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models

genphen

A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models

Bioconductor-mirror/genphen

A tool for quantification of associations between genotypes and phenotypes with statistical learning techniques such as random forests and support vector machines as well as with Bayesian inference using hierarchical models

Bioconductor-mirror/BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

InesdeSantiago/BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

BaalChIP

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

EBSeqHMM

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

Bioconductor-mirror/EBSeqHMM

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

lengning/EBSeqHMM

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

banocc

Bayesian ANalysis Of Compositional Covariance

Bioconductor-mirror/banocc

Bayesian ANalysis Of Compositional Covariance

george-weingart/banocc

Bayesian ANalysis Of Compositional Covariance

biobakery/banocc

Bayesian ANalysis Of Compositional Covariance

BASiCS

Bayesian Analysis of Single-Cell Sequencing data

catavallejos/BASiCS

Bayesian Analysis of Single-Cell Sequencing data

mfa

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

kieranrcampbell/mfa

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

ArnaudDroitLab/RJMCMCNucleosomes

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Bioconductor-mirror/RJMCMCNucleosomes

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

RJMCMCNucleosomes

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

ArnaudDroitLab/RJMCMC

Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bioconductor-mirror/birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

CNPBayes

Bayesian mixture models for copy number polymorphisms

scristia/CNPBayes

Bayesian mixture models for copy number polymorphisms

Bioconductor-mirror/CNPBayes

Bayesian mixture models for copy number polymorphisms

wmchad/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Bioconductor-mirror/BayesKnockdown

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

GRridge

Better prediction by use of co-data: Adaptive group-regularized ridge regression

markvdwiel/GRridge

Better prediction by use of co-data: Adaptive group-regularized ridge regression

Bioconductor-mirror/GRridge

Better prediction by use of co-data: Adaptive group-regularized ridge regression

Bioconductor-mirror/CSSP

ChIP-Seq Statistical Power

chandlerzuo/cssp

ChIP-Seq Statistical Power

CSSP

ChIP-Seq Statistical Power

Bioconductor-mirror/ctsGE

Clustering of Time Series Gene Expression data

ctsGE

Clustering of Time Series Gene Expression data

michmich76/ctsGE

Clustering of Time Series Gene Expression data

BUMHMM

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

alinaselega/BUMHMM

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

Bioconductor-mirror/BUMHMM

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

Bioconductor-mirror/bacon

Controlling bias and inflation in association studies using the empirical null distribution

bacon

Controlling bias and inflation in association studies using the empirical null distribution

Bioconductor-mirror/CoGAPS

Coordinated Gene Activity in Pattern Sets

CoGAPS

Coordinated Gene Activity in Pattern Sets

CoGAPS/CoGAPS

Coordinated Gene Activity in Pattern Sets

cdiener/dycone

dycone - analyze the dynamic landscape of metabolome data

Bioconductor-mirror/EBcoexpress

EBcoexpress for Differential Co-Expression Analysis

EBcoexpress

EBcoexpress for Differential Co-Expression Analysis

edgeR

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor-mirror/edgeR

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor-mirror/covEB

Empirical Bayes estimate of block diagonal covariance matrices

covEB

Empirical Bayes estimate of block diagonal covariance matrices

clarepacini/covEB

Empirical Bayes estimate of block diagonal covariance matrices

LFDREmpiricalBayes

Estimating Local False Discovery Rates Using Empirical Bayes Methods

Bioconductor-mirror/GRENITS

Gene Regulatory Network Inference Using Time Series

GRENITS

Gene Regulatory Network Inference Using Time Series

phenopath

Genomic trajectories with heterogeneous genetic and environmental backgrounds

affylmGUI

GUI for limma package with Affymetrix microarrays

Bioconductor-mirror/affylmGUI

GUI for limma package with Affymetrix microarrays

Bioconductor-mirror/limmaGUI

GUI for limma package with two color microarrays

limmaGUI

GUI for limma package with two color microarrays

Bioconductor-mirror/Clomial

Infers clonal composition of a tumor

Clomial

Infers clonal composition of a tumor

kieranrcampbell/ouija

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

kieranrcampbell/bnlfa

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

limma

Linear Models for Microarray Data

Bioconductor-mirror/limma

Linear Models for Microarray Data

florianerhard/lfc

Log fold change distribution tools for working with ratios of counts

Bioconductor-mirror/scDD

Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions

kdkorthauer/scDD

Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions

scDD

Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions

IoannisVardaxis/MACPET

Model based analysis for ChIA-PET data

andreaskapou/BPRMeth

Model higher-order methylation profiles

Bioconductor-mirror/BPRMeth

Model higher-order methylation profiles

andreaskapou/BPRMeth-devel

Model higher-order methylation profiles

BPRMeth

Model higher-order methylation profiles

MADSEQ

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Bioconductor-mirror/MADSEQ

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

ykong2/MADSEQ

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

normr

Normalization and difference calling in ChIP-seq data

your-highness/normR

Normalization and difference calling in ChIP-seq data

Bioconductor-mirror/normr

Normalization and difference calling in ChIP-seq data

kkdey/Logolas

Package for EDLogo visualization, featuring string logos and adaptive scaling of position weight matrices

PROPS

PRObabilistic Pathway Score (PROPS)

lhan22/PROPS

PRObabilistic Pathway Score (PROPS)

puma

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Bioconductor-mirror/puma

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

bd2kccd/r-causal

R-Causal Library

networkBMA

Regression-based network inference using Bayesian Model Averaging

Bioconductor-mirror/networkBMA

Regression-based network inference using Bayesian Model Averaging

RIVER

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

ipw012/RIVERpkg

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

ipw012/RIVER

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

Bioconductor-mirror/RIVER

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

wavClusteR

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

Bioconductor-mirror/wavClusteR

Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data

hms-dbmi/scde

Single Cell Differential Expression

scde

Single Cell Differential Expression

Bioconductor-mirror/scde

Single Cell Differential Expression

biobakery/sparseDOSSA

Sparse Data Observations for Simulating Synthetic Abundance

sparseDOSSA

Sparse Data Observations for Simulating Synthetic Abundance

Bioconductor-mirror/sparseDOSSA

Sparse Data Observations for Simulating Synthetic Abundance

Bioconductor-mirror/BitSeq

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

BitSeq

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

Bioconductor-mirror/tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression

Bioconductor-mirror/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

TRONCO

TRONCO, an R package for TRanslational ONCOlogy

BIMIB-DISCo/TRONCO

TRONCO, an R package for TRanslational ONCOlogy

mengyin/vashr

Variance Adaptive Shrinkage

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