Ephie Geza's activity
From 04/13/2023 to 05/12/2023
05/11/2023
- 04:27 PM Variant calling: detecting SNPs in WGS data relative to H37Rv 22.00 hours (Bug #156 (New): Debugging the bacterial variant calling pipeline)
- 04:27 PM Variant calling: detecting SNPs in WGS data relative to H37Rv Bug #156 (New): Debugging the bacterial variant calling pipeline
- Building the docker image from a dockerfile
- Changing of the Ubuntu distribution
- installing unzip, wget rena... - 04:02 PM Variant calling: detecting SNPs in WGS data relative to H37Rv 1.50 hour (Support #148 (New): Meeting: Results and discussion for 91_S91 (sample_1), 92_S92 (sample_2) and 93_S93)
- 03:42 PM Variant calling: detecting SNPs in WGS data relative to H37Rv 2.00 hours (Support #145 (New): Follow up on the feedback of the 17 November 2022 meeting)
- 03:38 PM Variant calling: detecting SNPs in WGS data relative to H37Rv 1.00 hour (Support #140 (New): Project for Mthawelanga on Redmine)
- 03:34 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection Support #155 (New): Cell type identification (manual) and annotation
- Use markers showing differential expression in each cluster to identify the cell types of each cluster
- 03:16 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection Support #154 (New): Gene expression levels
- To compile the genes and their expression levels. Rowsums of the expression data
- 03:12 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 1.00 hour (Support #149 (New): Adding Nyaradzo Chigorimbo-Tsikiwa on Redmine)
- 03:09 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 4.00 hours (Project: The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection)
- Initializing an renv project
- 03:00 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 24.00 hours (Support #153 (New): Data exploration)
- 02:59 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection Support #153 (New): Data exploration
- 1. Data pre-processing
1. Data normalization and scaling
1. Dimension reduction and clustering - 02:50 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 14.00 hours (Support #152 (New): Understanding the Slide seq data and analysis pipelines)
- 02:50 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection Support #152: Understanding the Slide seq data and analysis pipelines
- 1. Started by investigating the ssHippo data from the SeuratData package in R
- the data
- the code upto the crea... - 12:34 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection Support #152 (New): Understanding the Slide seq data and analysis pipelines
- This is to clarify whether single-cell RNA for the skin should be done or we use it as reference for slide seq analysis.
- 02:44 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 0.45 hour (Project: The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection)
- Discussing how to relax the gene filtering in FindMarkers function
- 12:41 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 1.00 hour (Project: The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection)
- Discussing preliminary findings
- 12:39 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 1.00 hour (Project: The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection)
- Meeting to discuss the reference single-cell of skin and spatial data
- 12:27 PM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection 1.00 hour (Project: The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection)
- Meeting to discuss the project proposal details and data
05/04/2023
- 11:51 AM The impact of aSTI on the foreskin: spatial transcriptome and ex vivo HIV-1 infection Support #149 (New): Adding Nyaradzo Chigorimbo-Tsikiwa on Redmine
- Hi Gerrit,
Kindly add Nyari on Redmine for **The impact of aSTI on the foreskin: spatial transcriptome and ex vivo...
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