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Fixed warning message
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@Jfortin1
Jfortin1 committed Oct 12, 2022
1 parent 8b2a14b commit d03c775
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4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -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 = "[email protected]", role = c("aut", "cre", "cph")))
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23 changes: 10 additions & 13 deletions inst/extdata/metadata.csv
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@@ -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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>","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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,character,FilePath,crisprScoreData/CasRxRF/RFcombined.rds
14 changes: 4 additions & 10 deletions inst/scripts/make-metadata.R
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Expand Up @@ -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, "\\.+.*"))
Expand All @@ -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).",
Expand All @@ -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,
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