Gantt

Support #165: Upload gVCFs and VCFS

Support #169: Update so far and way forward

Support #74: Uploading of data

Support #77: Testing pipeline on subset of data

Support #78: Proteomics raw data uploaded to Blackburn Lab researchdata

Support #79: Uploading new data from BGI

Support #80: Renaming all files according to the experiments

Support #81: Full run on ilifu of RNA seq pipeline

Support #82: Preliminary analysis of Proteome identification data

Support #85: MaxQuant run of raw proteomics data

Support #86: Analyze keloid proteomics data with mqmetaproteomics pipeline on ilifu

Support #90: QC of aligned reads

Support #92: Differential expression analysis

Feature #93: Improve normalization and imputaiton of tissue sample proteomics data and visualization

Support #100: Time seres analysis

Support #101: Secondary analysis: Transcription factor and pathway enrichment

Feature #103: Median group intensity added to output for visualization of proteomics target expression profiles

Feature #104: Summary table of mRNA and proteomics analysis for identified gene targets, protein level mean abundance per group added.

Support #159: Adding Adijat to the project

Support #113: QC of files

Support #114: Preparation of the reusable pipeline

Support #117: Variant calling

Support #138: 10 February 2022 meeting update and way forward

Support #139: Confirmation of the analysis to be conducted by the BST

Support #75: Taxonomic profiling using BLAST of identified proteins and peptides

Feature #69: Implement/adapt Tychus Nextflow pipeline

Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Feature #53: Setup a decontamination pipeline for Mark's project

Feature #54: DADA2 workflow as an additional option for processing 16S data

Support #45: Quality trimming with Trimmomatic

Support #38: How to download SRA files to hex

Bug #46: Read binning with CONCOCT

Support #27: What we already know and have setup

Support #50: Validate binning using single copy core genes

Support #60: Setup Nextflow metagenomics pipeline YAMP on hex

Support #24: Setting up the NGI-RNAseq pipeline on UCT Hex

Support #25: Configure NGI-RNAseq pipeline to run on hex

Support #30: Update Nextflow to version 0.27.6

Feature #12: Add more info in knowledge base categories

Feature #14: Add page describing different types of collaboration

Feature #33: Adding time tracking to the tickets

Feature #34: Add ticket type

Feature #134: Add captcha on ticket sumbission

Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample

Bug #56: Get pipeline details for getting data in and out.

Support #7: Support ticket 1

Bug #8: Bug ticket 1

Bug #9: Bug ticket 2

Support #10: Support ticket 2

Bug #41: Testing adding image inline

Bug #44: Testing category assignment

Bug #127: Testing mail sending

Support #151: Testing time records

Support #57: Perform proteomics differential abundance testing

Support #58: Pathway analysis

Support #152: Understanding the Slide seq data and analysis pipelines

Support #153: Data exploration

Support #149: Adding Nyaradzo Chigorimbo-Tsikiwa on Redmine

Support #154: Gene expression levels

Support #155: Cell type identification (manual) and annotation

Support #162: Adding Nontobeko and the Sabelo on Redmine

Support #164: Creating the project folder on ilifu

Support #140: Project for Mthawelanga on Redmine

Bug #156: Debugging the bacterial variant calling pipeline

Support #145: Follow up on the feedback of the 17 November 2022 meeting

Support #148: Meeting: Results and discussion for 91_S91 (sample_1), 92_S92 (sample_2) and 93_S93

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