{"id":24529010,"url":"https://github.com/saezlab/covid19","last_synced_at":"2026-01-01T21:55:51.669Z","repository":{"id":77872531,"uuid":"255854644","full_name":"saezlab/Covid19","owner":"saezlab","description":"We use our tools to analysis Covid19 RNAseq datasets","archived":false,"fork":false,"pushed_at":"2020-05-12T15:00:17.000Z","size":3218,"stargazers_count":4,"open_issues_count":1,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-01-22T07:37:38.283Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-04-15T08:34:55.000Z","updated_at":"2021-10-11T22:46:28.000Z","dependencies_parsed_at":"2023-03-04T02:45:47.483Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/Covid19","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCovid19","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCovid19/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCovid19/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCovid19/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/Covid19/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243769947,"owners_count":20345215,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-22T07:34:26.477Z","updated_at":"2026-01-01T21:55:46.639Z","avatar_url":"https://github.com/saezlab.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Applying Saezlab Tools to Covid-19 related Datasets\n\nThis repository contains the scripts used to apply some of our tools to Covid-19\nrelated datasets. In particular, we take the RNAseq data from the study: \n\n*\"SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems\"* \n\n\u003chttps://www.biorxiv.org/content/10.1101/2020.03.24.004655v1\u003e\n\n\u003chttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147507\u003e\n\nWe first focused in analysing the effect of SARS-CoV-2 infection in different \nhuman lung-related cells. \n\n+ Human lung epithelial cells (**NHBE**): mock treated vs infected with \nSARS-CoV-2. \n\n+ **A549** alveolar cancer cell line: mock treated vs infected with SARS-CoV-2.   \n\n+ **A549** cell line does not express ACE2, the receptor used by SARS-CoV-2 to \npenetrate into human cells. Therefore A549 were also transduced with **ACE2** \nand then mock treated or infected with SARS-CoV-2\n\n+ **Calu-3** human lung epithelial cancer cell line: mock treated vs \ninfected with SARS-CoV-2.  \n\nThen, we analysed the effects at the transcriptomic level of different viral \ninfections:\n\n+ A549 alveolar cancer cell line: mock treated vs infected with SARS-CoV-2.   \n\n+ A549 alveolar cancer cell line: mock treated vs infected with RSV. \n\n+ A549 alveolar cancer cell line: mock treated vs infected with HPIV3.\n\n## Effect of SARS-CoV-2 infection in different cell lines\n\nWe detail below the different scripts and analysis performed in this section:\n\n+ We first applied a traditional differential expression analysis using the \n**DESeq2** R package. This is aligned with the script of Agatha Treveil from \nTamas' group. \n\n\u003chttps://github.com/saezlab/Covid19/blob/master/DifferentialExpressionAnalysis.md\u003e\n\n+ Then, we used the normalised counts and the stastics generated in the previous \nscript to run **Dorothea** and **Progeny**. Doing so, we estimated Transcription\nfactors activity and pathway activity in the SARS-CoV-2 infected lines in \ncomparison with the mock treated. \n\n\u003chttps://github.com/saezlab/Covid19/blob/master/ProgenyDorothea.md\u003e\n\n+ We run **CARNIVAL** using different perturbations conditions related \nto the virus action. In order to do so, we used TF and Pathway activity scores \ngenerated in the previous script. CARNIVAL also requires a prior knowledge \nnetwork that was extracted from **Omnipath** using **OmnipathR** in line with\nthe network used by Dezso from Tamas' group. \n\n\u003chttps://github.com/saezlab/Covid19/blob/master/runCARNIVAL.md\u003e\n\n+ We perform a pathway enrichment analysis taking into account the nodes\nfrom **CARNIVAL** output.\n\n\u003chttps://github.com/saezlab/Covid19/blob/master/CarnivalEnrichment.md\u003e\n\n+ We are also exploring the cell cycle phase of the different samples.\n\n\u003chttps://github.com/saezlab/Covid19/blob/master/CellCycleStage.md\u003e\n\n## Effect of different viral infections on A549 cell line\n\nWe detail below the different scripts and analysis performed in this section:\n\n+ We first applied a traditional differential expression analysis using the \n**DESeq2** R package: \n\n\u003chttps://github.com/saezlab/Covid19/blob/master/ComparativeInfection/DifferentialExpressionAnalysis.md\u003e \n\n+ Then, we used the normalised counts and the stastics generated in the previous \nscript to run **Dorothea** and **Progeny**. Doing so, we estimated Transcription\nfactors activity and pathway activity in the SARS-CoV-2 infected lines in \ncomparison with the mock treated. \n\n\u003chttps://github.com/saezlab/Covid19/blob/master/ComparativeInfection/ProgenyDorothea.md\u003e\n\n+ We run **CARNIVAL** using different perturbations conditions related \nto the virus action. In order to do so, we used TF and Pathway activity scores \ngenerated in the previous script. CARNIVAL also requires a prior knowledge \nnetwork that was extracted from **Omnipath** using **OmnipathR** in line with\nthe network used by Dezso from Tamas' group. \n\n\u003chttps://github.com/saezlab/Covid19/blob/master/ComparativeInfection/runCARNIVAL.md\u003e\n\n+ We perform a pathway enrichment analysis taking into account the nodes\nfrom **CARNIVAL** output.\n\n\u003chttps://github.com/saezlab/Covid19/blob/master/ComparativeInfection/CarnivalEnrichment.md\u003e\n\n\n### License Info\n\nThis program is free software: you can redistribute it and/or modify it under \nthe terms of the GNU General Public License as published by the Free Software \nFoundation, either version 3 of the License, or (at your option) any later \nversion.\n\nThis program is distributed in the hope that it will be useful, but WITHOUT ANY \nWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR \nA PARTICULAR PURPOSE. See the GNU General Public License for more details.\n\nPlease check http://www.gnu.org/licenses/.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcovid19","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fcovid19","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcovid19/lists"}