dagmaraniedziela Goto Github PK
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dagmaraniedziela's Projects
amr_correlation
This is the code used to process fastq files of 147 bovine Escherichia coli isolates to de-novo assembled genomes, followed by screening for antimicrobial resistance genes and data analysis to correlate with phenotypic AMR data.
cicd_rinpharma
A repo for CI/CD in R packages workshop, R in Pharma 2022
rnaseq_fhepatica_ovine_pbmc
Analysis of an RNAseq dataset from sheep infected with liver fluke Fasciola hepatica.
rnaseq_saureus_cattle_infection
All code associated with my RNAseq analysis of two groups of cattle infected with different strains of Staphylococcus aureus. There is 5-6 cows in each group and transcriptomics data was analysed at 0, 24, 48, 72 and 168 hours post infection. The library preparation (polyA selected mRNA stranded libraries) and sequencing (paired end, sequencing depth 60M reads) was done by Macrogen. I used FastQC for quality control, fastp for trimming and STAR for alignment to Bos taurus genome UMD3.1 and creating gene counts.
salmonellambandaka
bash and R scripts used to analyse a comparative genomic data for S Mbandaka strains, and perform statistisc on phenotypic data
transcriptomics_and_pcastats
Code used to analyse data from Kalantar et al. (2022) sepsis transcriptomics dataset.
workshop-scrnaseq
Single cell RNA sequencing analysis course
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