R packages

ROTS: Reproducibility-optimized test statistic for differential expression analysis

Bioconductor link

SIVS: Iterative feature selection to shrink down the feature space into a small, yet robust set

CRAN link

PASI: Pathway Analysis for Sample-level Information utilizing pathway structures

GitHub link

ILoReg: High-resolution cell population identification from single-cell RNA-seq data

Bioconductor link

DCeN: Dynamically Co-expressed Neighborhoods for ranking genes in time-resolved gene expression profiling studies

Project link

EBSEA: Exon Based Strategy for differential Expression Analysis of genes in RNA-seq studies

Bioconductor link

scShaper: Linear trajectory inference from single-cell RNA-seq data

GitHub link

RODEO: Robust Deconvolution of cell-type specific gene expression profiles from bulk expression data

GitHub link

Phosphonormalizer: Compensation for normalization bias in phosphoproteomics

Bioconductor link

PowerExplorer: Power and sample size estimation tool for RNA-seq and quantitative proteomics studies

GitHub link

PAL: Pathway analysis of longitudinal transcriptomics and proteomics data

GitHub link

RepViz: Replicate oriented Visualization of chromatin and other genomic data

Bioconductor link

PECA: Peptide-level Expression Change Averaging for differential expression analysis in proteomics

Bioconductor link

RolDE: Robust longitudinal differential expression for proteomics

Bioconductor link

Other software

glaDIAtor: Untargeted analysis of data-independent acquisition mass spectrometry metaproteomics data

GitHub link

DIAtools: Toolset for analyzing data-independent acquisition mass spectrometry data

GitHub link

LC: Likelihood Contrasts for binary classification of longitudinal data

Project link

SimPhospho: Simulation of phosphopeptide spectra for confident phosphosite assignment

SourceForge link

PhosPiR: Automated pipeline for analyzingphosphoproteomics data

GitHub link

VarSCAT: Variant sequence context annotation toolkit

GitHub link

Webtools

COVID-19 browser: Exploring COVID-19 specific gene signature across multiple bulk and single-cell datasets

Shinyapps.io link

AHT risk calculator: Comparing the predicted risks of cardiovascular events and acute kidney injury between standard and intensive antihypertensive treatment

Shinyapps.io link

u-PA: Predicting biochemical recurrence of prostate cancer from longitudinal ultrasensitive-PSA data

Shinyapps.io link

Weightloss predictor: Predicting long-term weight changes from self-reported weight data

Shinyapps.io link