BRC_Organoid_Joana

Transcriptomic changes in organoid small intestinal epithelial cells upon interaction with lymphocytes

DB ID Project.id=6, Data.id=11

Scripts

header.R

header file with global variables and settings

01_createDbEntry.R

create database entries for the samples

02_fastQC.R

QA checks on the FASTQ files using the class CFastqQuality

03_trimmomatic_array_job.R

writes a batch array job for hpc to use trimmomatic for read trimming

04_fastQC_trimmed.R

QA checks on the trimmed FASTQ files using the class CFastqQuality

05_hisat2_array_job.R

create a parameter file and shell script to run array job on hpc

06_samtools_array_job.R

create a parameter file and shell script to run array job on hpc

07_bam_files_qa.R

quality checks on the bam files

08_counts_from_bams.R

generate count tables for transcripts from bam files

09_clustering_counts_matrix.R

cluster the samples based on count table

10_de_analysis.R

DE analysis for the count data using DESeq2

11_de_analysis_MCMC.R

DE analysis for the count data using a Bayesian approach by writing a log posterior function and optimizing the function using LearnBayes::laplace. The second half of the script has the option to use Stan to generate MCMC samples from the posterior.
nb_glm.stan Stan script, similar to the log posterior function. Can be used for genes that do not converge using optimizer.