brunocontrino/Doscheda

A DownStream Chemo-Proteomics Analysis Pipeline

brunocontrino/Doscheda

A DownStream Chemo-Proteomics Analysis Pipeline

Doscheda

A DownStream Chemo-Proteomics Analysis Pipeline

alussana/AffiXcan

A functional approach to impute Genetically Regulated Expression

GenoGAM

A GAM based framework for analysis of ChIP-Seq data

gstricker/fastGenoGAM

A GAM based framework for analysis of ChIP-Seq data

Bioconductor-mirror/GenoGAM

A GAM based framework for analysis of ChIP-Seq data

plantarum/flowPloidy

Analyze flow cytometer data to determine sample ploidy

Bioconductor-mirror/flowPloidy

Analyze flow cytometer data to determine sample ploidy

flowPloidy

Analyze flow cytometer data to determine sample ploidy

PathwaySplice

An R Package for Unbiased Splicing Pathway Analysis

SCCC-BBC/PathwaySplice

An R Package for Unbiased Splicing Pathway Analysis in RNAseq data

genphen

A tool for quantification of associations between genotypes and phenotypes with Bayesian inference and statistical learning techniques

snaketron/genphen

A tool for quantification of associations between genotypes and phenotypes with Bayesian inference and statistical learning techniques

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

flowQB

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

Bioconductor-mirror/flowQB

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

Bioconductor-mirror/birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

birte

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bioconductor-mirror/GRridge

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

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

rhondabacher/Trendy

Breakpoint analysis of time-course expression data

Trendy

Breakpoint analysis of time-course expression data

Bioconductor-mirror/CONFESS

Cell OrderiNg by FluorEScence Signal

CONFESS

Cell OrderiNg by FluorEScence Signal

gpls

Classification using generalized partial least squares

Bioconductor-mirror/gpls

Classification using generalized partial least squares

Bioconductor/gpls

Classification using generalized partial least squares

isarnassiri/CMEA

CMEA: An R package for Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile

sartorlab/chipenrich.data

Companion package to chipenrich

sevenC

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

ibn-salem/sevenC

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

ibn-salem/chromloop

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

alinaselega/BUMHMM

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

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

andrewthomasjones/EMMIXcontrasts

Contrasts in Mixed Effects for EMMIX Model with Random Effects

bacon

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

Bioconductor-mirror/bacon

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

timpeters82/consensus

Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

shenorrLab/csSAM

csSAM - cell-specific Significance Analysis of Microarrays

wilsoncai1992/adaptest

Data-Adaptive Statistics for High-Dimensional Multiple Testing

adaptest

Data-Adaptive Statistics for High-Dimensional Multiple Testing

Bioconductor-mirror/ENmix

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

xuz1/ENmix

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

ENmix

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

dmrseq

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

kdkorthauer/dmrseq

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

mikelove/DESeq2

Differential gene expression analysis based on the negative binomial distribution

DESeq2

Differential gene expression analysis based on the negative binomial distribution

edgeR

Empirical Analysis of Digital Gene Expression Data in R

Bioconductor-mirror/edgeR

Empirical Analysis of Digital Gene Expression Data in R

isglobal-brge/omicRexposome

Exposome and omic data associatin and integration analysis

omicRexposome

Exposome and omic data associatin and integration analysis

edge

Extraction of Differential Gene Expression

Bioconductor-mirror/edge

Extraction of Differential Gene Expression

jdstorey/edge

Extraction of Differential Gene Expression

StoreyLab/edge

Extraction of Differential Gene Expression

flipflop

Fast lasso-based isoform prediction as a flow problem

Bioconductor-mirror/flipflop

Fast lasso-based isoform prediction as a flow problem

PriceLab/trena-until-01mar2018

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

PriceLab/TReNA

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

PriceLab/trena

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

trena

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

TReNA

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

GEM

GEM: fast association study for the interplay of Gene, Environment and Methylation

fastGEM/GEM

GEM: fast association study for the interplay of Gene, Environment and Methylation

Bioconductor-mirror/GEM

GEM: fast association study for the interplay of Gene, Environment and Methylation

GENIE3

GEne Network Inference with Ensemble of trees

aertslab/GENIE3

GEne Network Inference with Ensemble of trees

ChrOertlin/anota2seq

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

anota2seq

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

reese3928/methylGO

Gene Set Analysis Using the Outcome of Differential Methylation

reese3928/methylGSA

Gene Set Analysis Using the Outcome of Differential Methylation

chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

Bioconductor-mirror/chipenrich

Gene Set Enrichment For ChIP-seq Peak Data

gespeR

Gene-Specific Phenotype EstimatoR

Bioconductor-mirror/gespeR

Gene-Specific Phenotype EstimatoR

cbg-ethz/gespeR

Gene-Specific Phenotype EstimatoR

zhushijia/GIGSEA

Genotype Imputed Gene Set Enrichment Analysis

rauschenberger/globalSeq

Global Test for Counts

hummelma/GlobalAncova

Global test for groups of variables via model comparisons

Bioconductor-mirror/affylmGUI

GUI for limma package with Affymetrix microarrays

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/GMRP

GWAS-based Mendelian Randomization and Path Analyses

GMRP

GWAS-based Mendelian Randomization and Path Analyses

Yuande/GMRP

GWAS-based Mendelian Randomization and Path Analyses

suchestoncampbelllab/survivR

gwasurvivr: an R package for genome wide survival analysis

suchestoncampbelllab/gwasurvivr

gwasurvivr: an R package for genome wide survival analysis

crbasel/hierinf

Hierarchical Inference

IVAS

Identification of genetic Variants affecting Alternative Splicing

Bioconductor-mirror/IVAS

Identification of genetic Variants affecting Alternative Splicing

tnaake/MetNet

Inferring metabolic networks from untargeted high-resolution mass spectrometry data

IMAS

Integrative analysis of Multi-omics data for Alternative Splicing

Bioconductor-mirror/IMAS

Integrative analysis of Multi-omics data for Alternative Splicing

hangost/IMAS

Integrative analysis of Multi-omics data for Alternative Splicing

Bioconductor-mirror/kebabs

Kernel-Based Analysis Of Biological Sequences

kebabs

Kernel-Based Analysis Of Biological Sequences

LEA

LEA: an R package for Landscape and Ecological Association Studies

Bioconductor-mirror/LEA

LEA: an R package for Landscape and Ecological Association Studies

Bioconductor-mirror/limma

Linear Models for Microarray Data

limma

Linear Models for Microarray Data

reedssorenson/RNAdecay

Maximum Likelihood Decay Modeling of RNA Degradation Data

RNAdecay

Maximum Likelihood Decay Modeling of RNA Degradation Data

reese3928/methylGOtemp

methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

andreaskapou/BPRMeth

Model higher-order methylation profiles

andreaskapou/BPRMeth2

Model higher-order methylation profiles

BPRMeth

Model higher-order methylation profiles

andreaskapou/BPRMeth-devel

Model higher-order methylation profiles

Bioconductor-mirror/BPRMeth

Model higher-order methylation profiles

QuackenbushLab/MONSTER

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

MoPS

MoPS - Model-based Periodicity Screening

Bioconductor-mirror/MoPS

MoPS - Model-based Periodicity Screening

gamerino/NBSplice

Negative Binomial Models to detect Differential Splicing

sysbiomed/glmSparseNet

Network Centrality Metrics for Elastic-Net Regularized Models

netReg

Network-Regularized Regression Models

OPWeight

Optimal p-value weighting with independent information

Bioconductor-mirror/OPWeight

Optimal p-value weighting with independent information

mshasan/OPWeight

Optimal p-value weighting with independent information

pmm

Parallel Mixed Model

Bioconductor-mirror/pmm

Parallel Mixed Model

SamGG/ropls

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

ropls

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

Bioconductor-mirror/ropls

PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

plrs

Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression

Bioconductor-mirror/plrs

Piecewise Linear Regression Splines (PLRS) for the association between DNA copy number and gene expression

JonBohlin/GAprediction

Prediction of gestational age with Illumina HumanMethylation450 data

Bioconductor-mirror/GAprediction

Prediction of gestational age with Illumina HumanMethylation450 data

GAprediction

Prediction of gestational age with Illumina HumanMethylation450 data

JonBohlin/predictGA

Prediction of gestational age with Illumina HumanMethylation450 data

GabrielHoffman/variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments

Bioconductor-mirror/variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments

variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments

hzc363/CytoDx

Robust prediction of clinical outcomes using cytometry data without cell gating

CytoDx

Robust prediction of clinical outcomes using cytometry data without cell gating

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)

RIVER

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

ipw012/RIVERpkg

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

izhbannikov/rqt

rqt: utilities for gene-level meta-analysis

rqt

rqt: utilities for gene-level meta-analysis

izhbannikov/rqt.bk

rqt: utilities for gene-level meta-analysis

Bioconductor-mirror/rqt

rqt: utilities for gene-level meta-analysis

tchitchek-lab/SPADEVizR

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

mlist/SPONGE

Sparse Partial Correlations On Gene Expression

SPONGE

Sparse Partial Correlations On Gene Expression

Bioconductor-mirror/NetCRG

SRGnet An R package for studying synergistic response genes from transcriptomics data

Bioconductor-mirror/SRGnet

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data

SRGnet

SRGnet: An R package for studying synergistic response to gene mutations from transcriptomics data from transcriptomics data

ZytoHMGU/CFAssay

Statistical analysis for the Colony Formation Assay

Bioconductor-mirror/CFAssay

Statistical analysis for the Colony Formation Assay

CFAssay

Statistical analysis for the Colony Formation Assay

cbg-ethz/knockdown

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

cbg-ethz/perturbatr

Statistical Analysis of High-Throughput Genetic Perturbation Screens

dirmeier/knockout

Statistical Analysis of High-Throughput Genetic Perturbation Screens

13479776/statTarget

Statistical Analysis of Metabolite Profile

statTarget

Statistical Analysis of Metabolite Profile

Bioconductor-mirror/statTarget

Statistical Analysis of Metabolite Profile

Bioconductor-mirror/SAGx

Statistical Analysis of the GeneChip

SAGx

Statistical Analysis of the GeneChip

SIAMCAT

Statistical Inference of Associations between Microbial Communities And host phenoTypes

zellerlab/siamcat

Statistical Inference of Associations between Microbial Communities And host phenoTypes

KonradZych/SIAMCAT

Statistical Inference of Associations between Microbial Communities And host phenoTypes

OscarBrock/gCrisprTools

Suite of Functions for Pooled Crispr Screen QC and Analysis

gCrisprTools

Suite of Functions for Pooled Crispr Screen QC and Analysis

Bioconductor-mirror/gCrisprTools

Suite of Functions for Pooled Crispr Screen QC and Analysis

metaCCA

Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

Bioconductor-mirror/metaCCA

Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

kieranrcampbell/switchde

Switch-like differential expression across single-cell trajectories

switchde

Switch-like differential expression across single-cell trajectories

Bioconductor-mirror/switchde

Switch-like differential expression across single-cell trajectories

Bioconductor-mirror/globalSeq

Testing for association between RNA-Seq and high-dimensional data

globalSeq

Testing for association between RNA-Seq and high-dimensional data

splineTimeR

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Bioconductor-mirror/splineTimeR

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

ZytoHMGU/splineTimeR

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Bioconductor-mirror/splineTCDiffExpr

biobroom

Turn Bioconductor objects into tidy data frames

StoreyLab/biobroom

Turn Bioconductor objects into tidy data frames

Bioconductor-mirror/biobroom

Turn Bioconductor objects into tidy data frames

superOmics/sparsenetgls

Using Gaussian graphical structue learning estimation in generalized least squared regression for multivariate normal regression

fmrs

Variable Selection in Finite Mixture of AFT Regression and FMR

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