This repository contains code which identifies tissue specific markers based on the GTEx and roadmap epigenomics project databases, as well as additional data from SRA and GEO.
The primary question that is being asked (and hopefully answered) is:
- How can we identify the source tissue of exosomes found in a peripheral fluid? 2. What are genes whose expression is particular to a tissue? 3. Knowing those genes, can we identify the source tissue of in silico generated exosome reads?
common_r
contains various R utilities for sub analysesexosome_reads
contains code to download placenta and various other tissue SRA experiments, perform an alignment, bias and subset the aligned reads to exosomes, and then call the resultant subset+biased bam files using cufflinks, and then pile all of the data up. See itsMakefile
for details.exosome_sra
contains code to examine reads from various extracellular vesicles from different tissue types. Currently not used for anything.go_analyses
contains the code to perform GO analyses on the basis of the identified tissue specific markers. See itsMakefile
for details.isrs_abstract
is an abstract for the Illinois Symposium on Reproductive Science which was acceptedmanuscript
contains the code to produce the paper based upon this work. See itsMakefile
for details.mk
contains various makefile settingsposter
contains the code for a poster which was presented at the Mayo Individualizing Medicine conference.rnaseq_workflow
is a git submodule which is the standard RNAseq workflowslides
is a selection of slides for the ISRS talktissue_expression
contains all of the code to build an R matrix of tissue expression across a large number of samples. See itsMakefile
for details.tissue_specific_expression
contains the code to turn the matrix of tissue expression into a list of genes which are possibly tissue specific and genes which are not by calculating τ. It also contains code to run SVM and other routines usingcaret
to do machine learning to identify source tissues.