[toc] # Bioinformatics Rome Bi-weekly meeting - [The community](https://bio-it.embl.de/bioinforome/) - [List of tools](https://pad.bio-it.embl.de/ybRlLkbXQn-ZTpMj2gnGHw) (started by Catrin Lloyd) ## Schedules and proposals - [2024](https://pad.bio-it.embl.de/_MendYueTnSF4mb7ZRywAw?view) - [2023 schedule and proposals](https://pad.bio-it.embl.de/AgKpxcVOTDiKbB4M-_wTMw) # :calendar: 8th of July 2024 :speaking_head_in_silhouette: Bobby Ranjan :dart: **Principal component analysis - part 6** :notebook: [Gitlab](https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial/-/blob/main/Eigenvalue_Decomposition.ipynb) :tv: [Recording](https://oc.embl.de/index.php/s/REAct0E4peG0pDp) :raising_hand: Attending: - Jasmina AlMousawi - Aileen Riesle - Sarah Kaspar - Alex Choromidis - Flavio Santilli - Francesco Tabaro - Sarah Kaspar Notes: - Proposals for future: 1. Bioinformatics lab meeting events 2. Clustering lecture series 3. Coding cafe 4. scRNA analysis - Concepts of data integration 5. Bayesian probability - UMAP and tSNE 6. Simpler coding sessions - Move to R 7. `apply` statements in R 8. Some bash - Logistics: - Fix a date - Perhaps Fri 15:30-17 # :calendar: 27th of June 2024 :speaking_head_in_silhouette: Bobby Ranjan :dart: **Principal component analysis - part 5** :notebook: :tv: [Recording](https://oc.embl.de/index.php/s/8z8SgAHV1AcWuvX) :raising_hand: Attending: - Jasmina AlMousawi - Falvio Santilli - Luca Michetti - Catrin Lloyd - Eva Geissen - Francesco Tabaro # :calendar: 3rd of May 2024 :speaking_head_in_silhouette: Bobby Ranjan :dart: **Principal component analysis - part 4** :notebook: :tv: [Recording](https://oc.embl.de/index.php/s/UkNFEzSibAoGjGe) :raising_hand: Attending: # :calendar: 22nd of March 2024 :speaking_head_in_silhouette: Bobby Ranjan :dart: **Principal component analysis - part 3** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial :tv: [Recording](https://oc.embl.de/index.php/s/8PjbtGbp1Z29bPR) :raising_hand: Attending: - Marzia Munafo' - Jasmina AlMousawi - Falvio Santilli - Aileen Riesle - Catrin Lloyd - Francesco Tabaro # :calendar: 29th of February 2024 :speaking_head_in_silhouette: Bobby Ranjan :dart: **Principal component analysis - part 2** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial :tv: [Recording](https://oc.embl.de/index.php/s/KSTB8C6OYjoADxO) :raising_hand: Attending: - Marzia Munafo' - Sofia Torchia - Jasmina AlMousawi - Falvio Santilli - Aileen Riesle - Luca Michetti - Joana Serrano - Francesco Tabaro # :calendar: 9th of February 2024 :speaking_head_in_silhouette: Bobby Ranjan :dart: **Principal component analysis - part 1** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial :tv: [Recording](https://oc.embl.de/index.php/s/WXW4EVsZM9FDm2y) # :calendar: 5th of December 2023 :speaking_head_in_silhouette: Francesco Tabaro and Bobby Ranjan :dart: **RNA-seq data analysis in Python - part 4** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial # :calendar: 16th of November 2023 :speaking_head_in_silhouette: Francesco Tabaro and Bobby Ranjan :dart: **RNA-seq data analysis in Python - part 3** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial # :calendar: 20th of October 2023 :speaking_head_in_silhouette: Francesco Tabaro and Bobby Ranjan :dart: **RNA-seq data analysis in Python - part 2** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial :raising_hand: Attending: 1. Catrin Lloyd 1. Luca Michetti 3. Aileen Riesle 4. Flavio Santilli 6. Tristan Weissalla :book: Notes: # :calendar: 4th of October 2023 :speaking_head_in_silhouette: Francesco Tabaro :dart: **RNA-seq data analysis in Python - part 1** :notebook: Material: https://git.embl.de/tabaro/bioinforome-rnaseq-python-tutorial :raising_hand: Attending: 1. Luca Michetti 2. Joana Serrano 3. Aileen Riesle 4. Flavio Santilli 5. Jasmina Al Mousawi 6. Tristan Weissalla 7. Bobby Ranjan :book: Notes: # :calendar: 6th of June 2023 :speaking_head_in_silhouette: Flavio Santilli :dart: **RNA-seq data analysis on tRFGG2 samples** :notebook: Material: :raising_hand: Attending: 1. Aileen Riesle 3. Flavio Santilli 7. Francesco Tabaro 8. Tristan Weissalla 9. Catrin Lloyd 3. Jasmina Al Mousawi :book: Notes: # :calendar: 22nd of May 2023 :speaking_head_in_silhouette: Tristan Wiessalla :dart: Segmentation and deconvolution of 2-photon image stacks :notebook: Material: :raising_hand: Attending: 1. Aileen Riesle 3. Flavio Santilli 4. Bobby Ranjan 7. Francesco Tabaro 8. Tristan Weissalla 9. Pietro Micheli 3. Jasmina Al Mousawi :book: Notes: # :calendar: 2nd of May 2023 :speaking_head_in_silhouette: Francesco Tabaro :dart: Padlock design for large scale Hyb-ISS experiments :notebook: Material: - [Slides](https://docs.google.com/presentation/d/1EyDAHgaRqCSYtyOoxxL4KlGMmgrFz3Gm1bWTo8_Hu40/edit?usp=sharing) - [Gitlab](https://git.embl.de/tabaro/padlock-design-parser/) :raising_hand: Attending: 1. Luca Michetti 2. Aileen Riesle 3. Flavio Santilli 4. Bobby Ranjan 6. Sara Formichetti 7. Francesco Tabaro 8. Basilia Acurzio :book: Notes: # :calendar: 12th of April 2023 :speaking_head_in_silhouette: Catrin Lloyd :dart: **Methylation Madness** - Epizoo DNA methylation analysis pipeline :notebook: Material: :raising_hand: Attending: 1. Luca Michetti 2. Aileen Riesle 3. Flavio Santilli 5. Jasmina Al Mousawi 6. Sara Formichetti 7. Francesco Tabaro :book: Notes: # :calendar: 30th of March 2023 :speaking_head_in_silhouette: Sara Formichetti :dart: **Differential allelic expression analysis from single embryo mRNA-Seq data pt 2** :notebook: Material: - [Slides](https://docs.google.com/presentation/d/1Sme4Zg0FN3HXFl0ZrNl4gUArRgX7nJWkxL0H1bz7yTI/edit?usp=sharing) - [snakemake pipeline](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/blob/main/snake-make/SNPsplit.Snakefile) - [snakemake config file for pipeline](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/tree/main/config/SNPsplit_config.yaml) - [snakemake config file for cluster](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/blob/main/config/SNPsplit_cluster.SLURM.json) - [SNPs tsv file (to see format) is here](https://drive.google.com/drive/folders/1pWfJzOk0hAGg58_MLVqeIGT8jXQp344X?usp=sharing) - [shell scripts used in Snakemake pipeline are here](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/tree/main/src/sh) - [Rmd of DESeq2 analysis w Sarah Kaspar is here](https://drive.google.com/drive/folders/1pWfJzOk0hAGg58_MLVqeIGT8jXQp344X?usp=sharing) :raising_hand: Attending: 1. Luca Michetti 2. Catrin Lloyd 3. Jasmina Al Mousawi 5. Francesco Tabaro 6. Bobby Ranjan :book: Notes: # :calendar: 16th of March 2023 :speaking_head_in_silhouette: Sara Formichetti :dart: **Differential allelic expression analysis from single embryo mRNA-Seq data** :notebook: Material: - [Slides](https://docs.google.com/presentation/d/1Sme4Zg0FN3HXFl0ZrNl4gUArRgX7nJWkxL0H1bz7yTI/edit?usp=sharing) - [snakemake pipeline](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/blob/main/snake-make/SNPsplit.Snakefile) - [snakemake config file for pipeline](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/tree/main/config/SNPsplit_config.yaml) - [snakemake config file for cluster](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/blob/main/config/SNPsplit_cluster.SLURM.json) - [SNPs tsv file (to see format) is here](https://drive.google.com/drive/folders/1pWfJzOk0hAGg58_MLVqeIGT8jXQp344X?usp=sharing) - [shell scripts used in Snakemake pipeline are here](https://git.embl.de/sformich/btgh_injected_blastocysts_smartseq/-/tree/main/src/sh) - [Rmd of DESeq2 analysis w Sarah Kaspar is here](https://drive.google.com/drive/folders/1pWfJzOk0hAGg58_MLVqeIGT8jXQp344X?usp=sharing) :raising_hand: Attending: 1. Aileen Riesle 2. Catrin Lloyd 3. Jasmina Al Mousawi 4. Flavio Santilli 5. Francesco Tabaro 6. Bobby Ranjan :book: Notes: # :calendar: 1st of March 2023 :speaking_head_in_silhouette: Jasmina Al Mousawi :dart: **ATAC and RNA-seq during EGA** :notebook: Material: :raising_hand: Attending: 1. Stylianos Tsagkris 2. Aileen Riesle 3. Jasmina Al Mousawi 4. Bobby Ranjan 5. Sara Formichetti 6. Flavio Santilli 7. Marzia Munafo 8. Catrin Lloyd 9. Luca Michetti 01. Francesco Tabaro :book: Notes: - 600 million reads! - pooled sequencing - two replicates per time points, four time points - call peaks on merged replicates, then find consensus peak set (bedtools intersect) on merged replicates over time points. - TOBIAS pipeline: https://www.nature.com/articles/s41467-020-18035-1 - TCseq: https://www.bioconductor.org/packages/release/bioc/html/TCseq.html - ChromHMM: https://www.nature.com/articles/nprot.2017.124 # :calendar: 14 February 2023 :speaking_head_in_silhouette: Bobby Ranjan :dart: **MetaboAnalystR pt. 2** :notebook: Material: - [R Tutorial](https://www.metaboanalyst.ca/docs/RTutorial.xhtml) - [Slides](https://drive.google.com/file/d/1LMqWaAm4eOPA1l1M3eGgrcw0G6uxSYzs/view?usp=sharing) - [GitLab Repository](https://git.embl.de/ranjan/metaboanalystr-tutorial/) :raising_hand: Attending: 1. Jasmina Al Mousawi 2. Stylianos Tsagkris 3. Luca Michetti 4. Catrin Lloyd 5. Sara Formichetti 6. Flavio Santilli 7. Francesco Tabaro :book: Notes: - Q: why 5000 is the minimum value in the dataset? Quantification answer filters peaks under this value. - Q: what's the mean-variance relationship? plot shows multiple degrees of correlation - LDA paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3310-7 # :calendar: 3 February 2023 :speaking_head_in_silhouette: Bobby Ranjan :dart: **MetaboAnalystR pt. 1** :notebook: Material: - [R Tutorial](https://www.metaboanalyst.ca/docs/RTutorial.xhtml) - [Slides](https://drive.google.com/file/d/1LMqWaAm4eOPA1l1M3eGgrcw0G6uxSYzs/view?usp=sharing) - [GitLab Repository](https://git.embl.de/ranjan/metaboanalystr-tutorial/) :raising_hand: Attending: - Luca Michetti - Flavio Santilli - Sara Formichetti - Aileen Riesle - Bobby Ranjan - Jasmina Al Mousawi - Catrin Lloyd (virtually) - Stylianos Tsagkris :book: Notes: * Jasmina: How to start analysis of unfamiliar data type? * Bobby: Tutorial (for package) gives some guidance. Normal distribution? * Jasmina: Sockets? (R studio context) * Bobby: allows you to connect to external server. In this case metabo * Unix Sockets are a special type of files that represent network connections * https://en.wikipedia.org/wiki/Unix_file_types * https://en.wikipedia.org/wiki/Unix_domain_socket * [Testing for sample variance](http://www.sthda.com/english/wiki/compare-multiple-sample-variances-in-r) # :calendar: 3 October 2022 :speaking_head_in_silhouette: Nicolas Descostes :dart: **Introduction to GitHub Actions** :notebook: Material: - [GitHub repo](https://github.com/descostesn/demodocker) :raising_hand: Attending: - Catrin - Bobby - Nicolas - Francesco - Sara :innocent: Apologies: - Tristan Questions: - Can you add Snakemake as a Conda env and run containerized Snakemake? - a bit clunky, better to enforce a [minimum Snakemake verions](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#depend-on-a-minimum-snakemake-version) # :calendar: 19 October 2022 :speaking_head_in_silhouette: Nicolas Descostes :dart: **Build Docker images in GitHub Actions** :notebook: Material: - [GitHub repo](https://github.com/descostesn/demodocker) :raising_hand: Attending: :innocent: Apologies: # :calendar: 3 October 2022 :speaking_head_in_silhouette: Nicolas Descostes :dart: **Introduction to GitHub Actions** :notebook: Material: - [GitHub repo](https://github.com/descostesn/demodocker) :raising_hand: Attending: - Catrin - Bobby - Nicolas - Francesco - Sara :innocent: Apologies: - Tristan Questions: - Can you add Snakemake as a Conda env and run containerized Snakemake? - a bit clunky, better to enforce a [minimum Snakemake verions](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#depend-on-a-minimum-snakemake-version) # :calendar: 19 September 2022 :speaking_head_in_silhouette: Tristan Weissalla :dart: **Overview of *in-vivo* calcium imaging data analysis and interactive dashboard** :notebook: Material: - NA :raising_hand: Attending: - Francesco - Nicolas - Severin - Tristan - Bobby - Catrin :innocent: Apologies: - Sara # :calendar: 9 September 2022 :speaking_head_in_silhouette: Francesco Tabaro :dart: **Snakemake: embedded package management and containerization** :notebook: Material: - [Gitlab repo](https://git.embl.de/tabaro/snakemake-playground) :raising_hand: Attending: - Bobby - Francesco - Irene - Nicolas - Sara - Tristan :innocent: Apologies: - NA # 6 April 2022 Presenter: Francesco Tabaro Subject: How I organize my snakemake pipelines Material: Live demo Script to retrieve all snakemake jobs IDs can be shared in https://git.embl.de/descoste/emblworkflowsandscripts/-/tree/main/scripts. Actions: 1) Create a Rome repository for singularities People are **highly encourage** to contribute by branching and merge request. Nicolas will maintain the repo. 2) Francesco showed how to create a git repo inside a git repo. It would be cool to write a post about it. # 15th March 2022 Presenter: Nicolas Descostes Subject: Creating subworkflows with snakemake Material: To come # 1st March 2022 Presenter: Nicolas Descostes Subject: Creating subworkflows with snakemake Material: To come # 10th February 2022 Presenter: Bobby Ranjan Subject: "DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data" Material: https://pubmed.ncbi.nlm.nih.gov/34615861/ Slides: https://docs.google.com/presentation/d/1oDYUpIBmziN3Go5TFxvsiMG48-LJ35fu/edit?usp=sharing&ouid=116548343669196990422&rtpof=true&sd=true # 16th November 2021 Presenter: Catrin Lloyd Subject: Allele-specific RNA-Seq Material: # 2nd November 2021 Presenter: Nicolas Descostes Subject: Good practices for reproducible bioinformatics Material: https://git.embl.de/descoste/project-backbone https://git.embl.de/descoste/emblworkflowsandscripts https://git.embl.de/descoste/reproducibleresearch # 19th October 2021 Presenter: Francesco Tabaro Subject: 1) General discussion on Bioinformatics practices 2) demo snakemake with CI Material: - https://pad.bio-it.embl.de/eNR_ad91SUC4MCPMoMOSBw# - https://git.embl.de/tabaro/snakemake-pipelines/-/tree/main