From c1d9ad0184ac2352497630e5690518547f46af14 Mon Sep 17 00:00:00 2001 From: marinaEM <47103829+marinaEM@users.noreply.github.com> Date: Wed, 4 Oct 2023 20:14:42 +0200 Subject: [PATCH 01/10] Update 04_read_filter_shap_drugbank.R Corrections to the drugbank drug effects simplifications --- scripts/r/04_read_filter_shap_drugbank.R | 62 ++++++------------------ 1 file changed, 14 insertions(+), 48 deletions(-) diff --git a/scripts/r/04_read_filter_shap_drugbank.R b/scripts/r/04_read_filter_shap_drugbank.R index cd8a4c3..ccddb89 100644 --- a/scripts/r/04_read_filter_shap_drugbank.R +++ b/scripts/r/04_read_filter_shap_drugbank.R @@ -171,50 +171,27 @@ drugbank_app_action <- merge(drugbank_app_action, entrez_uniprot,) %>% .[-which( length(unique(drugbank_app_action$entrez_id)) all(targets_shap_rel_stable$entrez %in% drugbank_app_action$entrez_id) ## check -saveRDS(drugbank_app_action, file.path(rds_folder, "drugbank_app_action_entrez.rds")) +saveRDS(drugbank_app_action, here("rds", "drugbank_app_action_entrez.rds")) + +drugbank_app_action$entrez_id <- as.character(drugbank_app_action$entrez_id) drugbank_app_action_genes <- merge(drugbank_app_action, genes_tr, by.x = "entrez_id", by.y = "entrez" ) ## Add the symbol column from the stable translate table -drugbank_app_action_genes$actions[drugbank_app_action_genes$actions == ""] <- "unknown" ## unify the not known drug actions to the same term "unknown" -drugbank_app_action_genes$actions[drugbank_app_action_genes$actions == "other"] <- "unknown" ## unify the not known drug actions to the same term "unknown" +drugbank_app_action_genes$actions[drugbank_app_action_genes$actions == ""] <- "Other" ## unify the not known drug actions to the same term "unknown" +drugbank_app_action_genes$actions[grep(drugbank_app_action$actions, pattern = "unknown|other/unknown")] <- "Other" ## unify the not known drug actions to the same term "unknown" any(is.na(drugbank_app_action_genes$actions)) -data.frame(table(drugbank_app_action_genes$actions)) - -drugbank_app_action_genes$simplified_action <- ifelse(drugbank_app_action_genes$actions == "ligand", "Ligand", - ifelse(drugbank_app_action_genes$actions == "adduct|binder", "Ligand", - ifelse(drugbank_app_action_genes$actions == "binder", "Ligand", - ifelse(drugbank_app_action_genes$actions == "binding", "Ligand", - ifelse(drugbank_app_action_genes$actions == "inverse agonist", "Modulator", - ifelse(drugbank_app_action_genes$actions == "allosteric modulator", "Modulator", - ifelse(drugbank_app_action_genes$actions == "antibody","Modulator", - ifelse(drugbank_app_action_genes$actions == "antagonist|partial agonist" , "Modulator", - ifelse(drugbank_app_action_genes$actions == "antagonist|agonist|negative modulator", "Modulator", - ifelse(drugbank_app_action_genes$actions == "antagonist|agonist", "Modulator", - ifelse(grepl("potentiator|agonist|activator|agonist\\|inducer|inducer|activator\\|modulator|substrate|stimulator|positive allosteric modulator|antisense oligonucleotide", drugbank_app_action_genes$actions), "Activator", - ifelse(grepl("other|chaperone|cleveage|substrate|oxidizer|deoxidizer|cofactor|neutralizer|gene replacement|incorporation into and destabilization|unknown|stabilization|product of|chaperone",drugbank_app_action_genes$actions), "other","Inhibitor")))))))))))) - +data.frame(table(drugbank_app_action_genes$actions))%>% write.table(., file = here("data","interim", "drug_actions.tsv"), sep = "\t", quote = F, col.names = T, row.names = F) ## Create drug effect table -length(unique(drugbank_app_action_genes$entrez_id)) ## We have all included KDTs 711 +drug_effects_translation <- fread(here("data","interim", "drug_actions_withSimplAction.csv")) ## Read edited table with simplified drug effect +drugbank_app_action_genes$simplified_action <- drug_effects_translation$Drug_eff_simpl[match(drugbank_app_action_genes$actions, drug_effects_translation$Var1)] -write.xlsx(drugbank_app_action_genes, file = file.path(tables_folder, "supp_tabl3_drugbank518_filtered.xlsx")) +length(unique(drugbank_app_action_genes$entrez_id)) ## We have all included KDTs 711 +write.xlsx(drugbank_app_action_genes, file = here("results", "tables", "supp_tabl3_drugbank518_filtered.xlsx")) alldrug_byaction <- drugbank_app_action_genes[,c("name", "actions", "entrez_id")] colnames(alldrug_byaction) <- c("drug", "drug_action", "KDT") - -## Simplify the drug action vector to 4 categories: "Activator", "Ligand", "Binder", "Inhibitor" -alldrug_byaction$Drug_effect <-ifelse(alldrug_byaction$drug_action == "ligand", "Ligand", - ifelse(alldrug_byaction$drug_action == "adduct|binder", "Ligand", - ifelse(alldrug_byaction$drug_action == "binder", "Ligand", - ifelse(alldrug_byaction$drug_action == "binding", "Ligand", - ifelse(alldrug_byaction$drug_action == "inverse agonist", "Modulator", - ifelse(alldrug_byaction$drug_action == "allosteric modulator", "Modulator", - ifelse(alldrug_byaction$drug_action == "antibody","Modulator", - ifelse(alldrug_byaction$drug_action == "antagonist|partial agonist" , "Modulator", - ifelse(alldrug_byaction$drug_action == "antagonist|agonist|negative modulator", "Modulator", - ifelse(alldrug_byaction$drug_action == "antagonist|agonist", "Modulator", - ifelse(grepl("potentiator|agonist|activator|agonist\\|inducer|inducer|activator\\|modulator|substrate|stimulator|positive allosteric modulator|antisense oligonucleotide", alldrug_byaction$drug_action), "Activator", - ifelse(grepl("other|chaperone|cleveage|substrate|oxidizer|deoxidizer|cofactor|neutralizer|gene replacement|incorporation into and destabilization|unknown|stabilization|product of|chaperone",alldrug_byaction$drug_action), "other","Inhibitor")))))))))))) - +## Add simplified drug effects +alldrug_byaction$Drug_effect <- drug_effects_translation$Drug_eff_simpl[match(alldrug_byaction$drug_action, drug_effects_translation$Var1)] alldrug_byaction$Drug_effect <- factor(alldrug_byaction$Drug_effect, levels = unique(alldrug_byaction$Drug_effect)) length(unique(alldrug_byaction$drug)) ## 1410 unique drugs alldrug_byaction$drugKDT <- paste0(alldrug_byaction$drug, alldrug_byaction$KDT) @@ -250,19 +227,8 @@ saveRDS(drugbank_effects_tar, file.path(rds_folder, "drugbank_effects_tar.rds")) ## Create a data frame to do Venn diagram of the simplified drug effects - RELEVANT DRUGS FILTERED BY DREXM3L drugs_rel_DF <- drugbank_effects_tar[, c("name", "actions", "symbol")] -drugs_rel_DF$Drug_effect <-ifelse(drugs_rel_DF$actions == "ligand", "Ligand", - ifelse(drugs_rel_DF$actions == "adduct|binder", "Ligand", - ifelse(drugs_rel_DF$actions == "binder", "Ligand", - ifelse(drugs_rel_DF$actions == "binding", "Ligand", - ifelse(drugs_rel_DF$actions == "inverse agonist", "Modulator", - ifelse(drugs_rel_DF$actions == "allosteric modulator", "Modulator", - ifelse(drugs_rel_DF$actions == "antibody","Modulator", - ifelse(drugs_rel_DF$actions == "antagonist|partial agonist" , "Modulator", - ifelse(drugs_rel_DF$actions== "antagonist|agonist|negative modulator", "Modulator", - ifelse(drugs_rel_DF$actions == "antagonist|agonist", "Modulator", - ifelse(grepl("potentiator|agonist|activator|agonist\\|inducer|inducer|activator\\|modulator|substrate|stimulator|positive allosteric modulator|antisense oligonucleotide", drugs_rel_DF$actions), "Activator", - ifelse(grepl("other|chaperone|cleveage|substrate|oxidizer|deoxidizer|cofactor|neutralizer|gene replacement|incorporation into and destabilization|unknown|stabilization|product of|chaperone",drugs_rel_DF$actions), "other","Inhibitor")))))))))))) - +drugs_rel_DF$Drug_effect <-drug_effects_translation$Drug_eff_simpl[match(drugs_rel_DF$actions, drug_effects_translation$Var1)] ## Add the simplified drug effects + df_venn_relevant <- drugs_rel_DF[, c("name","Drug_effect")] %>% add_column(value = as.numeric(1)) %>% dplyr::group_by(name, Drug_effect) %>% dplyr::summarise(n = dplyr::n(), .groups = "drop") %>% dplyr::filter(n >= 1L) %>% pivot_wider(names_from = Drug_effect, values_from = n ) %>% column_to_rownames("name") From 0ae6cbb57a2a2b93b849dfca47a489981f626405 Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Thu, 23 Nov 2023 19:33:07 +0100 Subject: [PATCH 02/10] Use an alternatice to zenodo-downloader. --- scripts/py/downloader.py | 61 ++++++++++++++++++++++++++++++++++++---- 1 file changed, 56 insertions(+), 5 deletions(-) diff --git a/scripts/py/downloader.py b/scripts/py/downloader.py index 4fdfc88..d46eb00 100644 --- a/scripts/py/downloader.py +++ b/scripts/py/downloader.py @@ -4,6 +4,11 @@ from pathlib import Path import tarfile +import pystow +import requests +from urllib.parse import quote + + DATA_REPOSITORY = Path(find_dotenv()).parent.joinpath("data") RAW_FOLDER = DATA_REPOSITORY.joinpath("raw") RAW_FOLDER.mkdir(exist_ok=True, parents=True) @@ -32,14 +37,60 @@ "expreset_pathvals_gtexV8.rds.feather" ] + +def get_latest_record(record_id): + """Get latest zenodo record ID from a given deposition identifier + + Parameters + ---------- + record_id : str + deposition identifier + + Returns + ------- + str + latest record ID + + """ + + url = requests.get(f"https://zenodo.org/records/{record_id}", timeout=10).url + return url.split("/")[-1] + + +def ensure_zenodo(name, record_id="6020480"): + """Ensure file availability and download it from zenodo + + Parameters + ---------- + name : str + file name + record_id : str + deposition identifier + + Returns + ------- + path : path-like + PosixPath to downloaded file + + """ + + record_id = get_latest_record(record_id) + print(name, quote(name)) + url = f"https://zenodo.org/records/{record_id}/files/{quote(name)}?download=1" + #url = f"{quote(url)}?download=1" + print(url) + + path = pystow.ensure("drexml", "datasets", record_id, url=url) + + return path + def download_files(record, files, folder): record = str(record) - zenodo = Zenodo() - - paths = [zenodo.download_latest(record, this_file) for this_file in files] + paths = [ensure_zenodo(this_file, record) for this_file in files] - for path in paths: + for path in paths: + print(path) if "localPDB" in path.name: this_file = tarfile.open(path.as_posix()) this_file.extractall(folder) @@ -48,5 +99,5 @@ def download_files(record, files, folder): if __name__ == "__main__": - download_files(7957439, rp_files, RAW_FOLDER) + download_files(7957438, rp_files, RAW_FOLDER) download_files(7737166, drexml_files, FINAL_FOLDER) From 4961547d2ef405dcdb438ea4ac1b96c1728f6a4e Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Thu, 23 Nov 2023 19:34:26 +0100 Subject: [PATCH 03/10] Fix derxml reference, use release 0.9.1.1. --- environment_drexml.yml | 2 +- environment_drexml_gpu.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment_drexml.yml b/environment_drexml.yml index 4c47bba..838bd01 100644 --- a/environment_drexml.yml +++ b/environment_drexml.yml @@ -26,4 +26,4 @@ dependencies: - xz=5.2.10 - zlib=1.2.13 - pip: - - git+https://github.com/loucerac/drexml.git@v0.9.9-retinitis \ No newline at end of file + - git+https://github.com/loucerac/drexml.git@v0.9.9.1-retinitis \ No newline at end of file diff --git a/environment_drexml_gpu.yml b/environment_drexml_gpu.yml index 1f25239..a3cfaa8 100644 --- a/environment_drexml_gpu.yml +++ b/environment_drexml_gpu.yml @@ -88,4 +88,4 @@ dependencies: - wheel=0.40.0 - xz=5.2.6 - pip: - - git+https://github.com/loucerac/drexml.git@v0.9.9-retinitis + - git+https://github.com/loucerac/drexml.git@v0.9.9.1-retinitis From 4d34d40f2a66f26aec810980ec6631a96db81a6a Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Fri, 24 Nov 2023 10:11:30 +0100 Subject: [PATCH 04/10] Fix paths. --- scripts/r/04_read_filter_shap_drugbank.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/scripts/r/04_read_filter_shap_drugbank.R b/scripts/r/04_read_filter_shap_drugbank.R index ccddb89..671a4cd 100644 --- a/scripts/r/04_read_filter_shap_drugbank.R +++ b/scripts/r/04_read_filter_shap_drugbank.R @@ -171,8 +171,7 @@ drugbank_app_action <- merge(drugbank_app_action, entrez_uniprot,) %>% .[-which( length(unique(drugbank_app_action$entrez_id)) all(targets_shap_rel_stable$entrez %in% drugbank_app_action$entrez_id) ## check - -saveRDS(drugbank_app_action, here("rds", "drugbank_app_action_entrez.rds")) +saveRDS(drugbank_app_action, file.path(rds_folder, "drugbank_app_action_entrez.rds")) drugbank_app_action$entrez_id <- as.character(drugbank_app_action$entrez_id) drugbank_app_action_genes <- merge(drugbank_app_action, genes_tr, by.x = "entrez_id", by.y = "entrez" ) ## Add the symbol column from the stable translate table @@ -185,7 +184,7 @@ drug_effects_translation <- fread(here("data","interim", "drug_actions_withSimpl drugbank_app_action_genes$simplified_action <- drug_effects_translation$Drug_eff_simpl[match(drugbank_app_action_genes$actions, drug_effects_translation$Var1)] length(unique(drugbank_app_action_genes$entrez_id)) ## We have all included KDTs 711 -write.xlsx(drugbank_app_action_genes, file = here("results", "tables", "supp_tabl3_drugbank518_filtered.xlsx")) +write.xlsx(drugbank_app_action_genes, file = file.path(tables_folder, "supp_tabl3_drugbank518_filtered.xlsx")) alldrug_byaction <- drugbank_app_action_genes[,c("name", "actions", "entrez_id")] colnames(alldrug_byaction) <- c("drug", "drug_action", "KDT") From 2d448ce74e0147b4650ee870567bd789352453bd Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Fri, 24 Nov 2023 10:19:53 +0100 Subject: [PATCH 05/10] Fix filtering. --- scripts/r/04_read_filter_shap_drugbank.R | 24 ++++-------------------- 1 file changed, 4 insertions(+), 20 deletions(-) diff --git a/scripts/r/04_read_filter_shap_drugbank.R b/scripts/r/04_read_filter_shap_drugbank.R index 671a4cd..675c436 100644 --- a/scripts/r/04_read_filter_shap_drugbank.R +++ b/scripts/r/04_read_filter_shap_drugbank.R @@ -195,8 +195,6 @@ alldrug_byaction$Drug_effect <- factor(alldrug_byaction$Drug_effect, levels = un length(unique(alldrug_byaction$drug)) ## 1410 unique drugs alldrug_byaction$drugKDT <- paste0(alldrug_byaction$drug, alldrug_byaction$KDT) -table(alldrug_byaction$Drug_effect) - df_venn <- alldrug_byaction[, c("drug","Drug_effect")] %>% add_column(value = as.numeric(1)) %>% dplyr::group_by(drug, Drug_effect) %>% dplyr::summarise(n = dplyr::n(), .groups = "drop") %>% @@ -210,7 +208,7 @@ png(filename = file.path(figures_folder,"venn_drugeffectsALL.png"), width = 8000 venn(df_venn, ilab=TRUE, zcolor = "style") dev.off() -#### 2. Filter and organize the drugs and their gene targets # +#### 4. Filter and organize the drugs and their gene targets # drugbank_effects_tar <- drugbank_app_action[which(drugbank_app_action$entrez_id %in% targets_shap_rel_stable$entrez), which(colnames(drugbank_app_action) %in% c("uniprot_id","drugbank_id","name", "type" , "groups", "categories", "description", "actions", "entrez_id" )) ] drugbank_effects_tar <- merge(drugbank_effects_tar, genes_tr, by.x = "entrez_id", by.y = "entrez" ) ## Add the symbol column from the stable translate table @@ -227,7 +225,7 @@ saveRDS(drugbank_effects_tar, file.path(rds_folder, "drugbank_effects_tar.rds")) drugs_rel_DF <- drugbank_effects_tar[, c("name", "actions", "symbol")] drugs_rel_DF$Drug_effect <-drug_effects_translation$Drug_eff_simpl[match(drugs_rel_DF$actions, drug_effects_translation$Var1)] ## Add the simplified drug effects - + df_venn_relevant <- drugs_rel_DF[, c("name","Drug_effect")] %>% add_column(value = as.numeric(1)) %>% dplyr::group_by(name, Drug_effect) %>% dplyr::summarise(n = dplyr::n(), .groups = "drop") %>% dplyr::filter(n >= 1L) %>% pivot_wider(names_from = Drug_effect, values_from = n ) %>% column_to_rownames("name") @@ -251,20 +249,8 @@ drug_ef <- data.frame( symbol = targets_shap_rel_stable$Gene_symbol, any(is.na(drug_ef)) table(drug_ef$Drug_effect) -## Simplify the drug action vector to 4 categories: "Activator", "Ligand", "Binder", "Inhibitor" -drug_ef$Drug_effect <- ifelse(drug_ef$Drug_effect == "ligand", "Ligand", - ifelse(drug_ef$Drug_effect == "adduct|binder", "Ligand", - ifelse(drug_ef$Drug_effect == "binder", "Ligand", - ifelse(drug_ef$Drug_effect == "binding", "Ligand", - ifelse(drug_ef$Drug_effect == "inverse agonist", "Modulator", - ifelse(drug_ef$Drug_effect == "allosteric modulator", "Modulator", - ifelse(drug_ef$Drug_effect == "antibody","Modulator", - ifelse(drug_ef$Drug_effect == "antagonist|partial agonist" , "Modulator", - ifelse(drug_ef$Drug_effect == "antagonist|agonist|negative modulator", "Modulator", - ifelse(drug_ef$Drug_effect == "antagonist|agonist", "Modulator", - ifelse(grepl("potentiator|agonist|activator|agonist\\|inducer|inducer|activator\\|modulator|substrate|stimulator|positive allosteric modulator|antisense oligonucleotide",drug_ef$Drug_effect ), "Activator", - ifelse(grepl("other|chaperone|cleveage|substrate|oxidizer|deoxidizer|cofactor|neutralizer|gene replacement|incorporation into and destabilization|unknown|stabilization|product of|chaperone",drug_ef$Drug_effect ), "other","Inhibitor")))))))))))) - +## Simplify the drug action vector to the selected categories: "Activator", "Ligand", "Other", "Inhibitor" +drug_ef$Drug_effect <-drug_effects_translation$Drug_eff_simpl[match(drug_ef$Drug_effect, drug_effects_translation$Var1)] ## Add the simplified drug effects dim(drug_ef) table(drug_ef$Drug_effect) @@ -272,5 +258,3 @@ table(drug_ef$Drug_effect) ## See which function is the most predominant for a certain gene KDT colnames(shap_relevant_stable)[!colnames(shap_relevant_stable) %in% drug_ef$symbol] ## Check that all KDTs have a drug effect write.table(drug_ef, file.path(tables_folder, "drugEffects_KDT_relevant_stable_simpl.tsv"), quote = F, sep = "\t", col.names = T, row.names = F) - - From b10bd5d317cf3c90c12ff40a1e98449f5b64c3e7 Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Fri, 24 Nov 2023 13:46:56 +0100 Subject: [PATCH 06/10] Add drug_actions_withSimplAction.csv to download list. --- scripts/py/downloader.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/py/downloader.py b/scripts/py/downloader.py index d46eb00..3387488 100644 --- a/scripts/py/downloader.py +++ b/scripts/py/downloader.py @@ -29,7 +29,8 @@ "physiological_paths.tsv", "physPathsAnnot.tsv", "WHO ATC-DDD 2021-12-03.csv", - "RP_map_functions_MPC-annot.xlsx" + "RP_map_functions_MPC-annot.xlsx", + "drug_actions_withSimplAction.csv" ] drexml_files = [ From 46ade5b7eb2b076aadae0fd32abd387da08de91d Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Fri, 24 Nov 2023 13:47:12 +0100 Subject: [PATCH 07/10] Read drug_actions_withSimplAction.csv from raw. --- scripts/r/04_read_filter_shap_drugbank.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/r/04_read_filter_shap_drugbank.R b/scripts/r/04_read_filter_shap_drugbank.R index 675c436..09efde1 100644 --- a/scripts/r/04_read_filter_shap_drugbank.R +++ b/scripts/r/04_read_filter_shap_drugbank.R @@ -180,7 +180,7 @@ drugbank_app_action_genes$actions[grep(drugbank_app_action$actions, pattern = "u any(is.na(drugbank_app_action_genes$actions)) data.frame(table(drugbank_app_action_genes$actions))%>% write.table(., file = here("data","interim", "drug_actions.tsv"), sep = "\t", quote = F, col.names = T, row.names = F) ## Create drug effect table -drug_effects_translation <- fread(here("data","interim", "drug_actions_withSimplAction.csv")) ## Read edited table with simplified drug effect +drug_effects_translation <- fread(here("data","raw", "drug_actions_withSimplAction.csv")) ## Read edited table with simplified drug effect drugbank_app_action_genes$simplified_action <- drug_effects_translation$Drug_eff_simpl[match(drugbank_app_action_genes$actions, drug_effects_translation$Var1)] length(unique(drugbank_app_action_genes$entrez_id)) ## We have all included KDTs 711 From e12d1eed525b2280e8b8f18850941fa139513140 Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Fri, 24 Nov 2023 13:48:18 +0100 Subject: [PATCH 08/10] Add drug_actions_withSimplAction.csv file. --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 441ebab..3c37cad 100644 --- a/README.md +++ b/README.md @@ -61,6 +61,11 @@ The necessary data to reproduce the results of the manuscript can be downloaded - File path: data/raw - Source: http://hipathia.babelomics.org/ +- Main actions by drug (manually curated): + - File name: drug_actions_withSimplAction.csv + - File path: data/raw + - Source: https://go.drugbank.com/releases + ## RP Mechanistic Map ![RP Mechanistic Map](./img/fig2_Pathway_Viewer_header.png) From f3262fe7237eda3f7360c659a1df594158871d4a Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Thu, 30 Nov 2023 10:03:19 +0100 Subject: [PATCH 09/10] Add version file. --- version.txt | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 version.txt diff --git a/version.txt b/version.txt new file mode 100644 index 0000000..b83ee08 --- /dev/null +++ b/version.txt @@ -0,0 +1,19 @@ +version=1.0.1 + DATA: + + Problem: Zenodo changed the way to use the API and required a developer token to use it. + + Solution: We have already solved this problem in the DREXML package and I have propagated the changes. We do not use the API, we use the download link resolution directly. + + DATA and CODE: + + Problem: In the review, a file was changed in the development branch and the changes were uploaded partially, making a change that required a new annotation file undetectable. The part that fails only affects the visualization of a heatmap. + + Solution: The complete code has been incorporated and the missing file has been uploaded to ZENODO. + + CODE: + + Problem: There was one dependency resolution that pulled from a library with an unresolvable version today. + + Solution: I created a patch on the version that was used in retinitis in the Python package and in the retinitis package it points to the patch. + From d26844d265496971e606874eb0751acdc41da550 Mon Sep 17 00:00:00 2001 From: Carlos Loucera Date: Thu, 30 Nov 2023 10:11:40 +0100 Subject: [PATCH 10/10] Update Zenodo link. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3c37cad..aa7db1f 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ ## Input Data -The necessary data to reproduce the results of the manuscript can be downloaded from [Zenodo](https://zenodo.org/record/7969017). Note that the workflow will try to automatically download the data after installing the dependencies. +The necessary data to reproduce the results of the manuscript can be downloaded from [Zenodo](https://zenodo.org/records/10203479). Note that the workflow will try to automatically download the data after installing the dependencies. - The Genotype-Tissue Expression (GTEx) RNA-Seq Data Gene read counts: - File name: GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_reads.gct