diff --git a/DESCRIPTION b/DESCRIPTION index 801d363..7a46164 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: crisprScoreData -Version: 1.1.3 -Date: 2022-06-16 +Version: 1.1.4 +Date: 2022-10-12 Title: Pre-trained models for the crisprScore package Authors@R: c( person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre", "cph"))) diff --git a/inst/extdata/metadata.csv b/inst/extdata/metadata.csv index cb8f359..a0f3d0f 100644 --- a/inst/extdata/metadata.csv +++ b/inst/extdata/metadata.csv @@ -1,13 +1,10 @@ -"Title","Description","BiocVersion","Genome","SourceType","SourceUrl","SourceVersion","Species","TaxonomyId","Coordinate_1_based","DataProvider","Maintainer","RDataClass","DispatchClass","RDataPath" -"DeepWt.hdf5","DeepHF pretrained model for widtype Cas9.","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/DeepHF/DeepWt.hdf5" -"DeepWt_T7.hdf5","DeepHF pretrained model for widtype Cas9 (T7 promoter).","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/DeepHF/DeepWt_T7.hdf5" -"DeepWt_U6.hdf5","DeepHF pretrained model for widtype Cas9 (U6 promoter).","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/DeepHF/DeepWt_U6.hdf5" -"esp_rnn_model.hdf5","DeepHF pretrained model for EspCas9.","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/DeepHF/esp_rnn_model.hdf5" -"hf_rnn_model.hdf5","DeepHF pretrained model for HFCas9.","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/DeepHF/hf_rnn_model.hdf5" -"Model_weights.pkl","Lindel pretrained model weights.","3.14",NA,"TXT","https://github.com/shendurelab/Lindel","1",NA,NA,TRUE,"University of Washington","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/Lindel/Model_weights.pkl" -"CRISPRa_model.pkl","Weissman pretrained model for CRISPRa.","3.14",NA,"TXT","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/Weissman/CRISPRa_model.pkl" -"CRISPRi_model.pkl","Weissman pretrained model for CRISPRi.","3.14",NA,"TXT","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/Weissman/CRISPRi_model.pkl" -"crispria_dnase_human_K562_hg38.bigWig","Processed DNase-seq data for K562 lifted to hg38","3.14",NA,"BigWig","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/Weissman/crispria_dnase_human_K562_hg38.bigWig" -"crispria_faire_human_K562_hg38.bigWig","Processed FAIRE-seq data for K562 lifted to hg38","3.14",NA,"BigWig","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/Weissman/crispria_faire_human_K562_hg38.bigWig" -"crispria_mnase_human_K562_hg38.bigWig","Processed MNase-seq data for K562 lifted to hg38","3.14",NA,"BigWig","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/Weissman/crispria_mnase_human_K562_hg38.bigWig" -"RFcombined.rds","CasRx-RF pretrained random forest model for CasRx.","3.14",NA,"RDS","https://gitlab.com/sanjanalab/cas13/","1",NA,NA,TRUE,"New York Genome Center","Jean-Philippe Fortin ","character","FilePath","crisprScoreData/CasRxRF/RFcombined.rds" +Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath +DeepWt.hdf5,DeepHF pretrained model for widtype Cas9.,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/DeepHF/DeepWt.hdf5 +DeepWt_T7.hdf5,DeepHF pretrained model for widtype Cas9 (T7 promoter).,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/DeepHF/DeepWt_T7.hdf5 +DeepWt_U6.hdf5,DeepHF pretrained model for widtype Cas9 (U6 promoter).,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/DeepHF/DeepWt_U6.hdf5 +esp_rnn_model.hdf5,DeepHF pretrained model for EspCas9.,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/DeepHF/esp_rnn_model.hdf5 +hf_rnn_model.hdf5,DeepHF pretrained model for HFCas9.,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/DeepHF/hf_rnn_model.hdf5 +Model_weights.pkl,Lindel pretrained model weights.,3.14,NA,TXT,https://github.com/shendurelab/Lindel,1,NA,NA,TRUE,University of Washington,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/Lindel/Model_weights.pkl +CRISPRa_model.pkl,Weissman pretrained model for CRISPRa.,3.14,NA,TXT,https://github.com/mhorlbeck/CRISPRiaDesign,1,NA,NA,TRUE,UCSF,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/Weissman/CRISPRa_model.pkl +CRISPRi_model.pkl,Weissman pretrained model for CRISPRi.,3.14,NA,TXT,https://github.com/mhorlbeck/CRISPRiaDesign,1,NA,NA,TRUE,UCSF,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/Weissman/CRISPRi_model.pkl +RFcombined.rds,CasRx-RF pretrained random forest model for CasRx.,3.14,NA,RDS,https://gitlab.com/sanjanalab/cas13/,1,NA,NA,TRUE,New York Genome Center,Jean-Philippe Fortin ,character,FilePath,crisprScoreData/CasRxRF/RFcombined.rds \ No newline at end of file diff --git a/inst/scripts/make-metadata.R b/inst/scripts/make-metadata.R index f8bfffe..41bc930 100644 --- a/inst/scripts/make-metadata.R +++ b/inst/scripts/make-metadata.R @@ -7,9 +7,6 @@ files <- c("DeepWt.hdf5", "Model_weights.pkl", "CRISPRa_model.pkl", "CRISPRi_model.pkl", - "crispria_dnase_human_K562_hg38.bigWig", - "crispria_faire_human_K562_hg38.bigWig", - "crispria_mnase_human_K562_hg38.bigWig", "RFcombined.rds") nfiles <- length(files) sources <- gsub("\\.","",str_extract(files, "\\.+.*")) @@ -22,7 +19,7 @@ url_weissman <- "https://github.com/mhorlbeck/CRISPRiaDesign" url_casrxrf <- "https://gitlab.com/sanjanalab/cas13/" urls <- c(rep(url_deephf,5), url_lindel, - rep(url_weissman,5), + rep(url_weissman,2), url_casrxrf) dess <- c("DeepHF pretrained model for widtype Cas9.", "DeepHF pretrained model for widtype Cas9 (T7 promoter).", @@ -32,19 +29,16 @@ dess <- c("DeepHF pretrained model for widtype Cas9.", "Lindel pretrained model weights.", "Weissman pretrained model for CRISPRa.", "Weissman pretrained model for CRISPRi.", - "Processed DNase-seq data for K562 lifted to hg38", - "Processed FAIRE-seq data for K562 lifted to hg38", - "Processed MNase-seq data for K562 lifted to hg38", "CasRx-RF pretrained random forest model for CasRx.") titles <- files providers <- c(rep("Fudan University", 5), "University of Washington", - rep("UCSF", 5), + rep("UCSF", 2), "New York Genome Center") paths1 <- paste0("crisprScoreData/DeepHF/", files[1:5]) paths2 <- paste0("crisprScoreData/Lindel/", files[6]) -paths3 <- paste0("crisprScoreData/Weissman/", files[7:11]) -paths4 <- paste0("crisprScoreData/CasRxRF/", files[12]) +paths3 <- paste0("crisprScoreData/Weissman/", files[7:9]) +paths4 <- paste0("crisprScoreData/CasRxRF/", files[10]) paths <- c(paths1, paths2, paths3, paths4) metadata <- data.frame(Title=titles,