Software by Katerina J. Kechris

KechrisLab GitHub

Omics Integration

• Omics Subtyping (R, Python, Tensorflow code: E. Stene, S. Helmi, L. Gillenwater) GitHub

  Multi-omics subtyping pipeline for chronic obstructive pulmonary disease. see Gillenwater et al., 2021

• SmCCNet (R package: J. Shi) GitHub CRAN

  Correlation analysis based method for discovering (quantitative) trait-specific multi-omics networks. see Shi et al., 2019

• Discordant (R package: C. Siska) GitHub Bioconductor

  Identify pairs of features that differentially correlate between phenotypic groups, with application to -omics data. see Siska et al., 2016 and Siska & Kechris, 2017.

• lcmix (R package: D. Dvorkin) R-Forge

  Hierarchical mixture models for genomic data integration. see Dvorkin et al., 2013.

  Metabolomics

• MSCAT Web Server at Metabolomics Workbench

  Database of metabolomics software tools and allows one to generate potential software workflows using an online interface. see Dekermanjian et al., 2021.

• MaRR (R package: T. Ghosh) GitHub Bioconductor

  Reproducibility of mass spectrometry based metabolomics data. see Ghosh et al., 2021

• MSPrep (R package: M. McGrath, G. Hughes) GitHub Bioconductor

  Post processing of LC/MS metabolomic data: Performs summarization of replicates, filtering, imputation, normalization, generates diagnostic plots and outputs final analytic datasets for downstream analysis. see Hughes et al., 2014.

  Microbiome

• tidyMicro (R package: C. Carpenter) GitHub CRAN

  A pipeline for microbiome data analysis and visualization using the tidyverse in R. see Carpenter et al., 2021

  Epigenetics

• comb-p (Python code: B. Pedersen) GitHub

  Combining genome-wide p-values using a modified Stouffer-Liptak test corrected for spatial correlations. see Kechris et al., 2010 and Pedersen et al., 2012

  Transcriptomics

• aptardi (Python: R. Lusk) GitHub

  Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence see Lusk et al., 2021

• MCMSeq (R package: B. Vestal, C. Moore) GitHub

  Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. see Vestal et al., 2020

• miR-MaGiC (Java/Snakemake pipeline: P. Russell) GitHub

  Pipeline for miRNA expression quantification from small RNA-seq see Russell et al., 2018

• HeritSeq (R package: J. Shi, P. Rudra, B. Vestal, P. Russell) GitHub CRAN

  Calculate heritability of count based expression traits derived from high-throughput sequencing experiments. see Rudra, Wen, Vestal et al., 2017

• multiMiR (R package: Y. Ru) Link to webserver GitHub Bioconductor

  Comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. see Ru et al., 2014.

  Transcription Factor Binding

• SULDEX (ANSI C++ code) Link to SULDEX Software at Pollock Lab

  Simultaneously analyze binding dissociation constants for large repertoires of sequences based on high throughput sequencing. see Pollock et al., 2011

• c-REDUCE (ANSI C code: assisted by D. Dvorkin) Available upon request

  c(onservation)-REDUCE: Extension of the REDUCE algorithm that incorporates conservation across multiple species to detect motifs that correlate with expression. see Kechris & Li, 2009

• OR-MEME (ANSI C code: M. Richards) Available upon request

  OR-MEME (Order Restricted MEME): Detecting DNA regulatory motifs by constraining the order of information content. see van Zwet et al., 2005

• TFEM (ANSI C code: M. Richards) Available upon request

  TFEM (Transcription Factor Expectation Maximization): Detecting DNA regulatory motifs by incorporating positional trends in information content. see Kechris et al., 2004