CshlSiepelLab/nascentRNASim

CshlSiepelLab/nascentRNASim

ChuanJ/posibatch

Adjust for positional and batch effects using ComBat

ChuanJ/JCPackage

Adjust for positional and batch effects using ComBat

kkdey/NMF0

A Fast Scalable and Flexible Non Negative Matrix Factorization Method

oneChannelGUI

A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

imkeller/gscreend

Analysis of pooled genetic screens

gscreend

Analysis of pooled genetic screens

SciDoPhenIA/phenomis

Analysis of single and multiple phenomic data sets

llrs/GSEAdv

Analyze Gene Sets Collections Properites

cx30/INDEED

An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

compomics/search-all-assess-subset

An implementation of the Search All, Asses Subset strategy for FDR estimation shotgun proteomics.

Caleb-Huo/differentialR2

An R package for circadian differential R2.

DiffCircaPipeline/Rpackage

An R package for DiffCircaPipeline: A framework for multifaceted characterization of differential rhythmicity

AWFisher

An R package for fast computing for adaptively weighted fisher's method

Caleb-Huo/AWFisher

An R package for fast computing for adaptively weighted fisher's method

wiscstatman/EBSeq

An R package for gene and isoform differential expression analysis of RNA-seq data

lengning/EBSeq

An R package for gene and isoform differential expression analysis of RNA-seq data

EBSeq

An R package for gene and isoform differential expression analysis of RNA-seq data

QUBIC

An R package for qualitative biclustering in support of gene co-expression analyses

OpenStats

A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

mpi2/OpenStats

A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

VingronLab/APL

Association Plots

elagralinska/APLpackage

Association Plots

ClemensKohl/APL

Association Plots

Winnie09/Lamian

a statistical framework for differential pseudotime analysis in multiple single-cell RNA-seq samples

biobakery/SparseDOSSA2

A Statistical Model for Describing and Simulating Microbial Community Profiles

peco

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

jhsiao999/peco

A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

iCARE

A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)

wheelerb/iCARE

A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)

BANDITS

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

SimoneTiberi/BANDITS

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

BUScorrect

Batch Effects Correction with Unknown Subtypes

XiangyuLuo/BUScorrect

Batch Effects Correction with Unknown Subtypes

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

athchen/beer

Bayesian Enrichment Estimation in R

RJMCMCNucleosomes

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

ArnaudDroitLab/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)

mpru/BIMEGA

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

SamirRachidZaim/binomialRF

Binomial Random Forest Feature Selection

binomialRF

Binomial Random Forest Feature Selection

shuyuzheng/synergyfinder

Calculate and Visualize Synergy Scores for Drug Combinations

synergyfinder

Calculate and Visualize Synergy Scores for Drug Combinations

Mulcom

Calculates Mulcom test

MolecularPathologyLab/MmCMS

Calling CMS for mouse tissue

DeMixT

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

wwylab/DeMixT

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

redsnic/CIMICE

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

lunacab/STATegRa

Classes and methods for multi-omics data integration

llrs/STATegRa

Classes and methods for multi-omics data integration

STATegRa

Classes and methods for multi-omics data integration

hdng/clonevol

Clonal ordering and visualization

FunChIP

Clustering and Alignment of ChIP-Seq peaks based on their shapes

CountClust

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

kkdey/CountClust

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

isarnassiri/CMEA

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

peterawe/CMScaller

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

broadinstitute/CommunityAMARETTO

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

Russel88/DAtest

Comparing Differential Abundance/Expression Methods

phosphonormalizer

Compensates for the bias introduced by median normalization in phosphoproteomics. This is done by taking enriched and non-enriched data and creating a normalization factor.

tchitchek-lab/CDS

Concomitant identification of distinctness and similarity in gene expression analysis.

ChristofSeiler/CytoGLMM

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

HiLDA

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

USCbiostats/HiLDA

Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

bacon

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

uds-helms/BEclear

Correction of batch effects in DNA methylation data

David-J-R/BEclear

Correction of batch effects in DNA methylation data

BEclear

Correction of batch effects in DNA methylation data

JackXu2333/rseAnalysis

Correlation analysis of RNA secondary structure mutation and differential expression

JackXu2333/dseAnalysis

Correlation analysis of RNA secondary structure mutation and differential expression

montilab/K2Taxonomer

Creating annotated submodules of high-throughput data through recursive partitioning

adam2o1o/treekoR

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

HelenaLC/CATALYST

Cytometry dATa anALYSis Tools

CATALYST

Cytometry dATa anALYSis Tools

rmpiro/decompTumor2Sig

Decomposition of individual tumors into mutational signatures by signature refitting

decompTumor2Sig

Decomposition of individual tumors into mutational signatures by signature refitting

CshlSiepelLab/DENR

Deconvolution of Expression for Nascent RNA Sequencing Data

CshlSiepelLab/tuSelecter2

Deconvolution of Expression for Nascent RNA Sequencing Data

saezlab/decoupleR

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

DeMAND

DeMAND

DASC

Detecting hidden batch factors through data adaptive adjustment for biological effects

aayushraman/DASC

Detecting hidden batch factors through data adaptive adjustment for biological effects

HaidYi/DASC

Detecting hidden batch factors through data adaptive adjustment for biological effects

zhanglabNKU/DASC

Detecting hidden batch factors through data adaptive adjustment for biological effects

ImpulseDE

Detection of DE genes in time series data using impulse models

YosefLab/ImpulseDE

Detection of DE genes in time series data using impulse models

JMF47/MDTS

Detection of de novo deletion in targeted sequencing trios

JMF47/DnMD

Detection of de novo deletion in targeted sequencing trios

MDTS

Detection of de novo deletion in targeted sequencing trios

BioQC

Detect tissue heterogeneity in expression profiles with gene sets

Accio/BioQC

Detect tissue heterogeneity in expression profiles with gene sets

LineagePulse

Differential expression analysis and model fitting for single-cell RNA-seq data

YosefLab/LineagePulse

Differential expression analysis and model fitting for single-cell RNA-seq data

ImpulseDE2

Differential expression analysis of longitudinal count data sets

YosefLab/ImpulseDE2

Differential expression analysis of longitudinal count data sets

Juananvg/DExMA

Differential Expression Meta-Analysis

SimoneTiberi/DifferentialRegulation

Differentially regulated genes from scRNA-seq data

mengchen18/omic3plus

Different methods for the integrative analysis multiple omics data

vjcitn/CSHstats

discussions and exercises on classical statistics for CSHL 2022

dcGSA

Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles

distinct

distinct: a method for differential analyses via hierarchical permutation tests

wikum/divergence.preSE

Divergence Computations

wikum/divergence

Divergence: Functionality for assessing omics data by divergence with respect to a baseline

divergence

Divergence: Functionality for assessing omics data by divergence with respect to a baseline

clarepacini/covEB

Empirical Bayes estimate of block diagonal covariance matrices

covEB

Empirical Bayes estimate of block diagonal covariance matrices

signeR

Empirical Bayesian approach to mutational signature discovery

rvalieris/signeR

Empirical Bayesian approach to mutational signature discovery

omicRexposome

Exposome and omic data associatin and integration analysis

isglobal-brge/omicRexposome

Exposome and omic data associatin and integration analysis

fabia

FABIA: Factor Analysis for Bicluster Acquisition

isarnassiri/FEVV

FEVV: Functional Enrichment of Genomic Variants and Variations

srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

mzytnicki/srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

cbg-ethz/TiMEx

Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

ballgown

Flexible, isoform-level differential expression analysis

alyssafrazee/ballgown

Flexible, isoform-level differential expression analysis

alyssafrazee/ballgown-release

Flexible, isoform-level differential expression analysis

llrs/BioCor

Functional similarities

BioCor

Functional similarities

DanrleyRF/SWeeP

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

DanrleyRF/rSWeeP

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

rSWeeP

Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

ArrayTools

geneChip Analysis Package

Zouter/triwise

Gene expression changes in three biological conditions

saeyslab/triwise

Gene expression changes in three biological conditions

Rommelio-coli/SSPA

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

SSPA

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

nucleoSim

Generate synthetic nucleosome maps

ArnaudDroitLab/nucleoSim

Generate synthetic nucleosome maps

GSAR

Gene Set Analysis in R

cpvSNP

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

geecc

Gene Set Enrichment Analysis Extended to Contingency Cubes

gsean

Gene Set Enrichment Analysis with Networks

dongminjung/gsean

Gene Set Enrichment Analysis with Networks

UW-GAC/genesis2

genesis assocation testing code rewrite

UW-GAC/genesis2_tests

genesis assocation testing code rewrite

GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

smgogarten/GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

UW-GAC/GENESIS

GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

favorov/GenometriCorr

Genometric Correlation package

BhaktiDwivedi/GISPA

GISPA: Method for Gene Integrated Set Profile Analysis

GISPA

GISPA: Method for Gene Integrated Set Profile Analysis

carter-allen/GPA

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

GPA

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

GGPA

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

garfield

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

GonzalezIgnacio/HandlingMissRows

Handling Missing Individuals in Multi-Omics Data Integration

missRows

Handling Missing Individuals in Multi-Omics Data Integration

GonzalezIgnacio/missRows

Handling Missing Individuals in Multi-Omics Data Integration

fspetale/fgga

Hierarchical ensemble method based on factor graph

zhengxwen/HIBAG

HLA Genotype Imputation with Attribute Bagging

HIBAG

HLA Genotype Imputation with Attribute Bagging

Rariant

Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

julian-gehring/Rariant

Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

RaikOtto/Uniquorn

Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

Uniquorn

Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

RaikOtto/Younikorn

Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

jingeyu/CTSV

Identification of cell-type-specific spatially variable genes accounting for excess zeros

IsoformSwitchAnalyzeR

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

kvittingseerup/IsoformSwitchAnalyzeR

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

aya49/flowGraph

Identifying differential cell populations in flow cytometry data accounting for marker frequency

broadinstitute/ImagingAMARETTO

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

andreamrau/padma

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

padma

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

broadinstitute/infercnv

Infer Copy Number Variation from Single-Cell RNA-Seq Data

infercnv

Infer Copy Number Variation from Single-Cell RNA-Seq Data

broadinstitute/inferCNV

Infer Copy Number Variation from Single-Cell RNA-Seq Data

dongminjung/PPInfer

Inferring functionally related proteins using protein interaction networks

PPInfer

Inferring functionally related proteins using protein interaction networks

kg737/INDEED_Patch

Integrated Differential Expression and Differential Network Analysis (INDEED)

ressomlab/INDEED

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

INDEED

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

vjcitn/bskl

interface to python sklearn via Rstudio reticulate

BiocSklearn

interface to python sklearn via Rstudio reticulate

vjcitn/BiocSklearn

interface to python sklearn via Rstudio reticulate

marziacremona/IWTomics

Interval-Wise Testing for Omics Data

IWTomics

Interval-Wise Testing for Omics Data

iteremoval

Iteration removal method for feature selection

cihga39871/iteremoval

Iteration removal method for feature selection

iterClust

Iterative Clustering

hd2326/iterClust

Iterative Clustering

UcarLab/iasva

Iteratively Adjusted Surrogate Variable Analysis

UcarLab/IA-SVA

Iteratively Adjusted Surrogate Variable Analysis

iasva

Iteratively Adjusted Surrogate Variable Analysis

joda

JODA algorithm for quantifying gene deregulation using knowledge

cbg-ethz/pathTiMEx

Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics

pasculescu/ClusterJudge

Judging Quality of Clustering Methods using Mutual Information

ClusterJudge

Judging Quality of Clustering Methods using Mutual Information

lol

Lots Of Lasso

MCbiclust

Massive correlating biclusters for gene expression data and associated methods

compmedlab/MCbiclust

Massive correlating biclusters for gene expression data and associated methods

rbentham/MCbiclust

Massive correlating biclusters for gene expression data and associated methods

MeasurementError.cor

Measurement Error model estimate for correlation coefficient

KechrisLab/MAI

Mechanism-Aware Imputation

hui-sheen/MetaGSCA

Meta-analysis of Gene Set differential Co-expression Analysis

MetaCyto

MetaCyto: A package for meta-analysis of cytometry data

hzc363/MetaCyto

MetaCyto: A package for meta-analysis of cytometry data

Haocan223/MetaGSCA

Meta Gene Set Co-expression Analysis

gevaertlab/MethylMix

MethylMix: Identifying methylation driven cancer genes

MethylMix

MethylMix: Identifying methylation driven cancer genes

gevaertlab/methylmix

MethylMix: Identifying methylation driven cancer genes

anjalisilva/mixMVPLN

Mixtures of Matrix Variate Poisson-log Normal Distributions

anjalisilva/MPLNClust

Mixtures of Multivariate Poisson-Log Normal Model for Clustering Count Data

mnmer

'(m,n)-mer' - A Simple Statistical Feature for Sequence Classification

MACPET

Model based analysis for paired-end data

IoannisVardaxis/MACPET

Model based analysis for paired-end data

dschlauch/MONSTER

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

QuackenbushLab/MONSTER

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

bhklab/mCI

Modified Concordance Index

bhklab/wCI

Modified Concordance Index

tdrose/mosbi

Molecular Signature identification using Biclustering

MultiBaC

Multiomic Batch effect Correction

ConesaLab/MultiBaC

Multiomic Batch effect Correction

mengchen18/mogsa

Multiple omics data integrative clustering and gene set analysis

mogsa

Multiple omics data integrative clustering and gene set analysis

HelenaLC/ddSingleCell

Multi-sample multi-group scRNA-seq data analysis tools

muscat

Multi-sample multi-group scRNA-seq data analysis tools

HelenaLC/muscat

Multi-sample multi-group scRNA-seq data analysis tools

gamerino/NBSplice

Negative Binomial Models to detect Differential Splicing

NBSplice

Negative Binomial Models to detect Differential Splicing

NeighborNet

Neighbor_net analysis

netboost

Network Analysis Supported by Boosting

xw187/MetID

Network-based prioritization of putative metabolite IDs

MetID

Network-based prioritization of putative metabolite IDs

ressomlab/MetID

Network-based prioritization of putative metabolite IDs

glmSparseNet

Network Centrality Metrics for Elastic-Net Regularized Models

sysbiomed/glmSparseNet

Network Centrality Metrics for Elastic-Net Regularized Models

netReg

Network-Regularized Regression Models

onlineFDR

Online error control

dsrobertson/onlineFDR

Online error rate control

Oscope

Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

PAIRADISE

PAIRADISE: Paired analysis of differential isoform expression

hubentu/PAIRADISE

PAIRADISE: Paired analysis of differential isoform expression

singha53/pandaR

PANDA Algorithm

jnpaulson/pandaR

PANDA Algorithm

pandaR

PANDA Algorithm

QuackenbushLab/pandaR

PANDA Algorithm

SNPRelate

Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

zhengxwen/SNPRelate

Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

kpj/dce

Pathway Enrichment Based on Differential Causal Effects

cbg-ethz/dce

Pathway Enrichment Based on Differential Causal Effects

cbg-ethz/pareg

Pathway enrichment using a regularized regression approach

CAnD

Perform Chromosomal Ancestry Differences (CAnD) Analyses

npGSEA

Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

adeschen/methylInheritance

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

methylInheritance

Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

EvaYiwenWang/PLSDAbatch

PLSDA-batch

VCCRI/Sierra

PolyA counting and differential transcript usage analysis for scRNA-seq data

PoTRA-Package/Development

PoTRA: Pathways of Topological Rank Analysis

PoTRA-Package/PoTRA

PoTRA: Pathways of Topological Rank Analysis

PoTRA

PoTRA: Pathways of Topological Rank Analysis

target

Predict Combined Function of Transcription Factors

sbhattacharya3/IntramiRExploreR

Predicting Targets for Drosophila Intragenic miRNAs

IntramiRExploreR

Predicting Targets for Drosophila Intragenic miRNAs

rfctbio-bsu/ORFhunteR

Predict open reading frames in nucleotide sequences

KrasnitzLab/CNprep

Pre-process DNA Copy Number (CN) Data for Detection of CN Events

SRenan/PING

Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

PING

Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data

profileScoreDist

Profile score distributions

yuhuihui2011/VaSP

Quantification and Visualization of Variations of Splicing in Population

yuhuihui2011/vasp

Quantification and Visualization of Variations of Splicing in Population

vasp

Quantification and Visualization of Variations of Splicing in Population

VaSP

Quantification and Visualization of Variations of Splicing in Population

yuhuihui2011/vasp_test

Quantification and Visulization of Variations of Splicing in Population

federicomarini/quantiseqr

Quantification of the Tumor Immune contexture from RNA-seq data

RGSEA

Random Gene Set Enrichment Analysis

randPack

Randomization routines for Clinical Trials

phettegger/randRotation

Random Rotation Methods for High Dimensional Data with Batch Structure

randRotation

Random Rotation Methods for High Dimensional Data with Batch Structure

RankProd

Rank Product method for identifying differentially expressed genes with application in meta-analysis

xinchoubiology/Rcppsva

Rcpp Integration Surrogate Variable Analysis

juanpegarcia/ROCpAI

Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

ROCpAI

Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

jingeyu/CSSN

Recovering spatially-varying cell-specific gene co-expression networks for single-cell spatial expression data.

ChristofSeiler/cytoeffect

Regression Models with Multivariate Outcomes for Mass Cytometry Experiments

AMARETTO

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

broadinstitute/PerturbationAMARETTO

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

gevaertlab/AMARETTO

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

waldronlab/lefser

R implementation of the LEfSE method for microbiome biomarker discovery

lefser

R implementation of the LEfSE method for microbiome biomarker discovery

tweeDEseq

RNA-seq data analysis using the Poisson-Tweedie family of distributions

isglobal-brge/EpiMutations

Robust outlier identification for DNA methylation data

isglobal-brge/epimutacions

Robust outlier identification for DNA methylation data

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

Genentech/midasHLA

R package for immunogenomics data handling and association analysis

Genentech/MiDAS

R package for immunogenomics data handling and association analysis

rqt

rqt: utilities for gene-level meta-analysis

izhbannikov/rqt.bk

rqt: utilities for gene-level meta-analysis

izhbannikov/rqt

rqt: utilities for gene-level meta-analysis

Rtreemix

Rtreemix: Mutagenetic trees mixture models.

RUVnormalize

RUV for normalization of expression array data

SAIGEgds

Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies

leekgroup/fdrreg

Science-wise false discovery rate and proportion of true null hypotheses estimation

swfdr

Science-wise false discovery rate and proportion of true null hypotheses estimation

leekgroup/swfdr

Science-wise false discovery rate and proportion of true null hypotheses estimation

selectKSigs

Selecting the number of mutational signatures using a perplexity-based measure and cross-validation

ndukler/tuSelecter2

Selecting transcript model using PRO-seq

jdgagnon/plotGrouper

Shiny app GUI wrapper for ggplot with built-in statistical analysis

plotGrouper

Shiny app GUI wrapper for ggplot with built-in statistical analysis

safe

Significance Analysis of Function and Expression

lgeistlinger/safe

Significance Analysis of Function and Expression

methInheritSim

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

belleau/methInheritSim

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

belleau/methylInheritanceSim

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

BIMSBbioinfo/deconvR

Simulation and Deconvolution of Omic Profiles

hms-dbmi/scde

Single Cell Differential Expression

scde

Single Cell Differential Expression

SomaticSignatures

Somatic Signatures

comm03/trysomesigs

Somatic Signatures

julian-gehring/SomaticSignatures

Somatic Signatures

tchitchek-lab/SPADEVizR

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

TrigosTeam/spaSim

Spatial point data simulator for tissue images

MarcElosua/SPOTlight

`SPOTlight`: Spatial Transcriptomics Deconvolution

SRGnet

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

isarnassiri/SRGnet

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

GeneSelector

Stability and Aggregation of ranked gene lists

statOmics/stageR

stageR: stage-wise analysis of high throughput gene expression data in R

stageR

stageR: stage-wise analysis of high throughput gene expression data in R

YosefLab/MPRAnalyze

Statistical Analysis of MPRA data

MPRAnalyze

Statistical Analysis of MPRA data

PhenStat

Statistical analysis of phenotypic data

HDTD

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

AnestisTouloumis/HDTD

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

goncalves-lab/waddR

Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

waddR

Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

goncalves-lab/diffexpR

Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

TitanCNA

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

gavinha/TitanCNA

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

ATLi2001/titancna

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

survtype

Subtype Identification with Survival Data

acichonska/metaCCA

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

metaCCA

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

hendriau/Summix

Summix: A method to estimate and adjust for population structure in genetic summary data

jtleek/sva-devel

Surrogate Variable Analysis

steveneschrich/msva

Surrogate Variable Analysis

sva

Surrogate Variable Analysis

timma

Target Inhibition Interaction using Maximization and Minimization Averaging

TCGAbiolinksGUI

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

BioinformaticsFMRP/TCGAbiolinksGUI

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

pageRank

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

hd2326/pageRank

Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

SiminaB/MultiMed

Testing multiple biological mediators simultaneously

MultiMed

Testing multiple biological mediators simultaneously

jasonserviss/ClusterSignificance

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

ClusterSignificance

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

siskac/discordant

The Discordant Method: A Novel Approach for Differential Correlation

discordant

The Discordant Method: A Novel Approach for Differential Correlation

Harman

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

JasonR055/Harman

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

AnnaLaddach/TrajectoryGeometry

This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

deltaCaptureC

This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

michaeldshapiro/deltaCaptureC

This Package Discovers Meso-scale Chromatin Remodeling from 3C Data

cbg-ethz/TMixClust

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

TMixClust

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

mklarqvist/rtomahawk

Tools for computing, querying and storing linkage-disequilibrium data

pcastellanoescuder/POMA_package

Tools for Omics Data Analysis

pcastellanoescuder/POMA

Tools for Omics Data Analysis

JMF47/recountNNLS

Transcript abundance linear modeling from compressed coverage information

TFARM

Transcription Factors Association Rules Miner

gaiac/TFARM

Transcription Factors Association Rules Miner

LiubaNM/TFARM

Transcription Factors Association Rules Miner

receptLoss

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

dpique/receptLoss

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

EmpiricalBrownsMethod

Uses Brown's method to combine p-values from dependent tests

switchBox

Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

marchion/switchBox

Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

VSOLassoBag

Variable Selection Oriented LASSO Bagging Algorithm

likelet/LassoBag

Variable Selection Oriented LASSO Bagging Algorithm

likelet/lassoBag

Variable Selection Oriented LASSO Bagging Algorithm

mengyin/vashr

Variance Adaptive Shrinkage

oirot/tumorHeatmap

Visual comparison of mutational processes in a set of tumors

LiNk-NY/package

What the Package Does (One Line, Title Case)

SRenan/XCIR

XCI-inference

XCIR

XCI-inference

YAPSA

Yet Another Package for Signature Analysis

slw287r/yapsa

Yet Another Package for Signature Analysis

eilslabs/YAPSA

Yet Another Package for Signature Analysis

huebschm/YAPSA

Yet Another Package for Signature Analysis

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