# Ademola/Ruth Weekly Meetings from November 2022 ## About the format: ### Copy the content below and provide an update _What did you achieve last week?_ _Who did you help last week?_ _Who helped you last week?_ _What did you struggle with?_ _What would you like to work on this week?_ _Where do you need help?_ ## 04th November 2022 **Ruth Nanjala** _What did you achieve last week?_ - Optimizing a Nextflow pipeline for HLA typing - Wrote a Nextflow pipeline for the GMS course NGS pipeline - TAing for the NGS course _Who did you help last week?_ - GMS MSc students _Who helped you last week?_ - Yang (Supervisor) _What did you struggle with?_ - Estimating HLA allele frequencies _What would you like to work on this week?_ - Estimating HLA allele frequencies - Estimating HLA allele diversity - Meet with departmental DGS - Weekly lab meeting and one-on-one meeting - GMS statistical course - Bayesian Statistics _Where do you need help?_ - Estimating HLA allele frequencies **Ademola Ayeinuro** _What did you achieve last week?_ _Who did you help last week?_ _Who helped you last week?_ _What did you struggle with?_ _What would you like to work on this week?_ - Quantify T Cells - Finish up figures for manuscript _Where do you need help?_ ## 12th November 2022 **Ruth Nanjala** _What did you achieve last week?_ - Estimated HLA allele frequencies - Met with departmental DGS - Weekly lab meeting and one-on-one meeting - GMS statistical course - Bayesian Statistics _Who did you help last week?_ - N/A _Who helped you last week?_ - Yang (Supervisor) - Esther - Kevin _What did you struggle with?_ - Estimating HLA allele diversity _What would you like to work on this week?_ - Estimating HLA allele diversity - GMS statistical course - Population genetics - Do pop gen analysis - Weekly one-on-one meeting _Where do you need help?_ - GWAS analysis **Ademola Emmanuel** _What did you achieve last week?_ - I improved my image analysis using a new software, hence would have to start analysing my images all over again _Who did you help last week?_ _Who helped you last week?_ _What did you struggle with?_ _What would you like to work on this week?_ - Quantify T Cells - Finish up figures for manuscript _Where do you need help?_ ## 19th November 20222 **Ruth Nanjala** _What did you achieve last week?_ - GMS statistical course - Advanced GWAS - Modifying HLA allele frequencies plots - Ploting allele coverage plots - Weekly one-on-one meeting - Reviewing AfriSoc mentorship applications - Reviewing Rachel's & Rose applications _What did you struggle with?_ - Plotting _What would you like to work on this week?_ - Estimating HLA allele diversity - Meet with the BMRC team - Modifying allele frequency plots - Weekly one-on-one meeting - PCA analysis - [ ] genome-wide PCA - [ ] genome-wide PCA projected onto 1000 Genomes samples - [ ] IBD within samples - [ ] merge Gambian dataset and 1000G AFR samples and project them onto the same PC - [ ] PCA within MHC region **Ademola Aiyenuro** _What would you like to work on this week_ - Manuscript text- - Improve the results section - Manuscript figures - Send off my samples for DDL typing # 25th November 2022 **Ruth Nanjala** _What did you achieve last week?_ - Estimating HLA allele diversity - Meet with the BMRC team - Modifying allele frequency plots - Weekly one-on-one meeting _What did you struggle with?_ - IBD computation using plink _What would you like to work on this week?_ - Project progress presentation - GMS course - Machine learning & Statistical models for polygenic traits - Redo frequency plots - Design PCA plots Count the number of immune cells in a cancer infected cell