Activity

From 06/20/2019 to 07/19/2019

06:38 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Feature #93 (Resolved): Improve normalization and imputaiton of tissue sample proteomics data and visualization: 1) configurable normalization method (eg median, quantiles)
2) configurable imputation method (eg bayes PCA, KNN)
3... Thys Potgieter

11:37 AM Pathogen outbreak study - Pseudomonas single isolate WGS Check coverage cutoffs for SNP analysis: SNP analysis is done with freebayes (on quality trimmed and filtered reads) with default settings ( -C 2 -min_coverag... Katie Lennard

02:12 PM Microbiota profiling of cows milk with and without traditional fermentation Data processed with dada2 pipeline on Ilifu: Both read trim strategies and taxonomic DB used will be considered to try and improve species-level resolution compar... Katie Lennard
11:36 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #90: QC of aligned reads: When the differential expression analysis was run, the samples were clustering in two distinct groups.
Looking in... Jon Ambler
11:28 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #92 (In Progress): Differential expression analysis: A list of the top differentially expressed genes have been created for the tissue data set.
This set includes gene... Jon Ambler
09:22 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #86 (Resolved): Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu: Thys Potgieter
09:16 AM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #85 (Resolved): MaxQuant run of raw proteomics data: Thys Potgieter

01:02 PM Microbiota profiling of cows milk with and without traditional fermentation Meetin with Pieter and Mike to discuss analysis: Mainly they are looking for improved species-level resolution with a few specific species they are hoping to see. I w... Katie Lennard

05:21 PM The impact of fire and herbivores on soil microbes dada2 testrun on HPC successfull: Config files edited by user (on HPC copy of repo). https://github.com/kviljoen/16S-rDNA-dada2-pipeline/blob/master/co... Katie Lennard

04:42 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #92: Differential expression analysis: Including this into the first python script so merging and splitting by experiment into the required files takes plac... Jon Ambler
04:40 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #92: Differential expression analysis: Writing a script for this in python for repeatability. Jon Ambler
04:38 PM Identification of biomarkers in keloids and folliculitis keloidalis nuchae (FKN) Support #92 (Resolved): Differential expression analysis: Conduct differential expression analysis on the samples.
The experiments are outlined in the RNAseq_analysis_8_Ma... Jon Ambler

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