fix "version_avaliable" to "version_available"

JhuangLab · Nov 20, 2018 · 4c033c7 · 4c033c7
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,7 @@
+2018-11-20 Li Jianfeng <[email protected]>
+
+		* fix "version_avaliable" to "version_available"
+
 2018-11-13 Li Jianfeng <[email protected]>
 
 		* change samtools and htslib source_url t codeload

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BioInstaller
 Title: Integrator of Bioinformatics Resources
-Version: 0.3.6.3001
+Version: 0.3.7
 Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Maintainer: Jianfeng Li <[email protected]>
 Description:

diff --git a/README.md b/README.md
@@ -72,15 +72,19 @@ devtools::install_github("JhuangLab/BioInstaller")
 ```
 ## Shiny UI overview
 
+**Note**, the Shiny application of BioInstaller was migrated to [bioshiny](https://github.com/ngsjs/bioshiny) project. All shiny files in this package will deprecated soon.
+
+In the new project, we will provides one-click method (command line and Shiny UI) to create bioshiny application and its plugins. We are also developing more free plugins of bioshiny for various bioinformatics data analysis. 
+
 ```
 # Start the standalone Shiny application
 BioInstaller::web(auto_create = TRUE)
 ```
 
-<img src="https://raw.githubusercontent.com/Miachol/ftp/master/files/images/bioinstaller/overview1.jpg" align="middle" />
-
 <img src="https://raw.githubusercontent.com/Miachol/ftp/master/files/images/bioinstaller/overview2.jpg" align="middle" />
 
+<img src="https://raw.githubusercontent.com/Miachol/ftp/master/files/images/bioinstaller/overview1.jpg" align="middle" />
+
 <img src="https://raw.githubusercontent.com/Miachol/ftp/master/files/images/bioinstaller/overview3.jpg" align="middle" />
 
 <img src="https://raw.githubusercontent.com/Miachol/ftp/master/files/images/bioinstaller/overview4.jpg" align="middle" />

diff --git a/inst/extdata/config/db/db_main.toml b/inst/extdata/config/db/db_main.toml
@@ -346,58 +346,55 @@ version_available = ["allAnnotatedVariants", "allActionableVariants"]
 
 [db_mirdb]
 source_url = "http://mirdb.org/download/miRDB_v{{version}}_prediction_result.txt.gz"
-version_avaliable = ["5.0", "4.0", "3.0", "2.0", "1.0"]
+version_available = ["5.0", "4.0", "3.0", "2.0", "1.0"]
 
 [db_mirtarbase]
 source_url = "http://mirtarbase.mbc.nctu.edu.tw/cache/download/{{version}}/miRTarBase_MTI.xlsx"
-version_avaliable = ["7.0"]
+version_available = ["7.0"]
 
 [db_mirnest]
 source_url = "http://rhesus.amu.edu.pl/mirnest/copy/downloads/{{version}}.gz"
-version_avaliable = ["mirnest_EST_predictions", "mirnest_targets", "mirnest_deep_predictions",
+version_available = ["mirnest_EST_predictions", "mirnest_targets", "mirnest_deep_predictions",
                                   "mirnest_degradomes", "mirnest_mirtrons", "mirnest_mirna_gene_structure"]
 
 [db_rbpdb]
 source_url = "http://rbpdb.ccbr.utoronto.ca/downloads/{{version}}"
-version_avaliable = ["RBPDB_v1.3.1_2012-11-21.sql", "RBPDB_v1.3.1_2012-11-21_TDT.zip",
+version_available = ["RBPDB_v1.3.1_2012-11-21.sql", "RBPDB_v1.3.1_2012-11-21_TDT.zip",
                                   "RBPDB_v1.3.1_2012-11-21_CSV.zip"]
 
 [db_appris]
 source_url = "http://apprisws.bioinfo.cnio.es/pub/current_release/datafiles/homo_sapiens/{{version}}/appris_data.principal.txt"
-version_avaliable = ["GRCh38", "rs108v26", "up201703v26", "a1v26", "GRCh37", "rs105v24", "g12v24"]
+version_available = ["GRCh38", "rs108v26", "up201703v26", "a1v26", "GRCh37", "rs105v24", "g12v24"]
 
 [db_lncipedia]
 source_url = "https://lncipedia.org/downloads/lncipedia_{{version}}"
-version_avaliable = ["5_1_hg19.bed", "5_1_hg38.bed", "5_1_hc_hg19.bed", "5_1_hc_hg38.bed",
-                                  "5_1.fasta", "5_1_hc.fasta", "5_1_hg19.gff", "5_1_hg38.gff", "5_1_hc_hg19.gff",
-                                  "5_1_hc_hg38.gff", "5_1_hg19.gtf", "5_1_hg38.gtf", "5_1_hc_hg19.gtf",
-                                  "5_1_hc_hg38.gtf"]
+version_available = "!!glue {strsplit('@>@str <- c('%s_hg19.bed', '%s_hg38.bed', '%s_hc_hg19.bed', '%s_hc_hg38.bed', '%s.fasta', '%s_hc.fasta', '%s_hg19.gff', '%s_hg38.gff', '%s_hc_hg19.gff', '%s_hc_hg38.gff', '%s_hg19.gtf', '%s_hg38.gtf', '%s_hc_hg19.gtf', '%s_hc_hg38.gtf'); c(sprintf(str, '5_1'), sprintf(str, '5_2'))@<@', ' ')[[1]]}"
 
 [db_msigdb]
 source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/msigdb/{{version}}"
-version_avaliable = ["c1.all.v6.2.entrez.gmt", "c1.all.v6.2.symbols.gmt", "c2.all.v6.2.entrez.gmt", "c2.all.v6.2.symbols.gmt", "c2.cgp.v6.2.entrez.gmt", "c2.cgp.v6.2.symbols.gmt", "c2.cp.biocarta.v6.2.entrez.gmt", "c2.cp.biocarta.v6.2.symbols.gmt", "c2.cp.kegg.v6.2.entrez.gmt", "c2.cp.kegg.v6.2.symbols.gmt", "c2.cp.reactome.v6.2.entrez.gmt", "c2.cp.reactome.v6.2.symbols.gmt", "c2.cp.v6.2.entrez.gmt", "c2.cp.v6.2.symbols.gmt", "c3.all.v6.2.entrez.gmt", "c3.all.v6.2.symbols.gmt", "c3.mir.v6.2.entrez.gmt", "c3.mir.v6.2.symbols.gmt", "c3.tft.v6.2.entrez.gmt", "c3.tft.v6.2.symbols.gmt", "c4.all.v6.2.entrez.gmt", "c4.all.v6.2.symbols.gmt", "c4.cgn.v6.2.entrez.gmt", "c4.cgn.v6.2.symbols.gmt", "c4.cm.v6.2.entrez.gmt", "c4.cm.v6.2.symbols.gmt", "c5.all.v6.2.entrez.gmt", "c5.all.v6.2.symbols.gmt", "c5.bp.v6.2.entrez.gmt", "c5.bp.v6.2.symbols.gmt", "c5.cc.v6.2.entrez.gmt", "c5.cc.v6.2.symbols.gmt", "c5.mf.v6.2.entrez.gmt", "c5.mf.v6.2.symbols.gmt", "c6.all.v6.2.entrez.gmt", "c6.all.v6.2.symbols.gmt", "c7.all.v6.2.entrez.gmt", "c7.all.v6.2.symbols.gmt", "msigdb.v6.2.entrez.gmt", "msigdb.v6.2.symbols.gmt", "msigdb_v3.0.zip", "msigdb_v3.1.zip", "msigdb_v4.0.zip", "msigdb_v5.0.zip", "msigdb_v5.1.zip", "msigdb_v5.1_chip.zip", "msigdb_v5.2.zip", "msigdb_v5.2_chip.zip", "msigdb_v6.0.zip", "msigdb_v6.0_chip.zip", "msigdb_v6.1.zip", "msigdb_v6.1_chip.zip", "msigdb_v6.2.xml", "msigdb_v6.2.zip"]
+version_available = ["c1.all.v6.2.entrez.gmt", "c1.all.v6.2.symbols.gmt", "c2.all.v6.2.entrez.gmt", "c2.all.v6.2.symbols.gmt", "c2.cgp.v6.2.entrez.gmt", "c2.cgp.v6.2.symbols.gmt", "c2.cp.biocarta.v6.2.entrez.gmt", "c2.cp.biocarta.v6.2.symbols.gmt", "c2.cp.kegg.v6.2.entrez.gmt", "c2.cp.kegg.v6.2.symbols.gmt", "c2.cp.reactome.v6.2.entrez.gmt", "c2.cp.reactome.v6.2.symbols.gmt", "c2.cp.v6.2.entrez.gmt", "c2.cp.v6.2.symbols.gmt", "c3.all.v6.2.entrez.gmt", "c3.all.v6.2.symbols.gmt", "c3.mir.v6.2.entrez.gmt", "c3.mir.v6.2.symbols.gmt", "c3.tft.v6.2.entrez.gmt", "c3.tft.v6.2.symbols.gmt", "c4.all.v6.2.entrez.gmt", "c4.all.v6.2.symbols.gmt", "c4.cgn.v6.2.entrez.gmt", "c4.cgn.v6.2.symbols.gmt", "c4.cm.v6.2.entrez.gmt", "c4.cm.v6.2.symbols.gmt", "c5.all.v6.2.entrez.gmt", "c5.all.v6.2.symbols.gmt", "c5.bp.v6.2.entrez.gmt", "c5.bp.v6.2.symbols.gmt", "c5.cc.v6.2.entrez.gmt", "c5.cc.v6.2.symbols.gmt", "c5.mf.v6.2.entrez.gmt", "c5.mf.v6.2.symbols.gmt", "c6.all.v6.2.entrez.gmt", "c6.all.v6.2.symbols.gmt", "c7.all.v6.2.entrez.gmt", "c7.all.v6.2.symbols.gmt", "msigdb.v6.2.entrez.gmt", "msigdb.v6.2.symbols.gmt", "msigdb_v3.0.zip", "msigdb_v3.1.zip", "msigdb_v4.0.zip", "msigdb_v5.0.zip", "msigdb_v5.1.zip", "msigdb_v5.1_chip.zip", "msigdb_v5.2.zip", "msigdb_v5.2_chip.zip", "msigdb_v6.0.zip", "msigdb_v6.0_chip.zip", "msigdb_v6.1.zip", "msigdb_v6.1_chip.zip", "msigdb_v6.2.xml", "msigdb_v6.2.zip"]
 
 [db_mircancer]
 source_url = "http://mircancer.ecu.edu/downloads/{{version}}.txt"
-version_avaliable = ["miRCancerOctober2017", "miRCancerMarch2017", "miRCancerDecember2016", "miRCancerSeptember2016", "miRCancerJune2016", "miRCancerMarch2016", "miRCancerDecember2015", "miRCancerSeptember2015", "miRCancerJune2015", "miRCancerMarch2015", "miRCancerDecember2014", "miRCancerSeptember2014", "miRCancerJune2014", "miRCancerMarch2014", "miRCancerDecember2013", "miRCancerSeptember2013", "miRCancerJune2013", "miRCancerMarch2013", "miRCancerNovember2012"]
+version_available = ["miRCancerOctober2017", "miRCancerMarch2017", "miRCancerDecember2016", "miRCancerSeptember2016", "miRCancerJune2016", "miRCancerMarch2016", "miRCancerDecember2015", "miRCancerSeptember2015", "miRCancerJune2015", "miRCancerMarch2015", "miRCancerDecember2014", "miRCancerSeptember2014", "miRCancerJune2014", "miRCancerMarch2014", "miRCancerDecember2013", "miRCancerSeptember2013", "miRCancerJune2013", "miRCancerMarch2013", "miRCancerNovember2012"]
 
 [db_dcdb]
 source_url = "http://www.cls.zju.edu.cn/dcdb/downloadfile/{{version}}.zip"
-version_avaliable = ["DCDB2_plaintxt", "DCDB2.sql", "targets", "Drug_combinations",
+version_available = ["DCDB2_plaintxt", "DCDB2.sql", "targets", "Drug_combinations",
                                   "components_identifier"]
 
 [db_oncomirdb]
 source_url = "http://lifeome.net/database/oncomirdb/oncomirdb.v-{{version}}_download.txt"
-version_avaliable = "1.1-20131217"
+version_available = "1.1-20131217"
 
 [db_islandviewer]
 source_url = "http://www.pathogenomics.sfu.ca/islandviewer/download/datasets/all_gis_{{version}}.txt.tar.gz"
-version_avaliable = ["islandviewer_iv4", "islandpick_iv4", "islandpath_dimob_iv4",
+version_available = ["islandviewer_iv4", "islandpick_iv4", "islandpath_dimob_iv4",
                                   "sigi_hmm_iv4", "islander_iv4"]
 
 [db_hpdi]
 source_url = "http://bioinfo.wilmer.jhu.edu/PDI/{{version}}"
-version_avaliable = ["protein_chip_full_seq.csv", "protein_annotation.txt",
+version_available = ["protein_chip_full_seq.csv", "protein_annotation.txt",
                                   "pro2motif.txt", "DNA_motifs.txt", "motif2protein.txt",
                                   "all_pwm.zip", "all_gpr_files.zip", "supplemental.pdf"]
 
@@ -450,3 +447,11 @@ version_available = ["ewas_singlemarker", "GO_Category", "KEGG_Pathway"]
 [db_cancersplicingqtl]
 source_url = "http://www.cancersplicingqtl-hust.com/downloads/{{version}}.xlsx"
 version_available = ["ACC_sQTLs", "BLCA_sQTLs", "BRCA_sQTLs", "CESC_sQTLs", "CHOL_sQTLs", "COAD_sQTLs", "DLBC_sQTLs", "ESCA_sQTLs", "GBM_sQTLs", "HNSC_sQTLs", "KICH_sQTLs", "KIRC_sQTLs", "KIRP_sQTLs", "LAML_sQTLs", "LGG_sQTLs", "LIHC_sQTLs", "LUAD_sQTLs", "LUSC_sQTLs", "MESO_sQTLs", "OV_sQTLs", "PAAD_sQTLs", "PCPG_sQTLs", "PRAD_sQTLs", "READ_sQTLs", "SARC_sQTLs", "SKCM_sQTLs", "STAD_sQTLs", "TGCT_sQTLs", "THCA_sQTLs", "THYM_sQTLs", "UCEC_sQTLs", "UCS_sQTLs", "UVM_sQTLs", "ACC_Survival_sQTLs", "BLCA_Survival_sQTLs", "BRCA_Survival_sQTLs", "CESC_Survival_sQTLs", "CHOL_Survival_sQTLs", "COAD_Survival_sQTLs", "DLBC_Survival_sQTLs", "ESCA_Survival_sQTLs", "GBM_Survival_sQTLs", "HNSC_Survival_sQTLs", "KICH_Survival_sQTLs", "KIRC_Survival_sQTLs", "KIRP_Survival_sQTLs", "LAML_Survival_sQTLs", "LGG_Survival_sQTLs", "LIHC_Survival_sQTLs", "LUAD_Survival_sQTLs", "LUSC_Survival_sQTLs", "MESO_Survival_sQTLs", "OV_Survival_sQTLs", "PAAD_Survival_sQTLs", "PCPG_Survival_sQTLs", "PRAD_Survival_sQTLs", "READ_Survival_sQTLs", "SARC_Survival_sQTLs", "SKCM_Survival_sQTLs", "STAD_Survival_sQTLs", "TGCT_Survival_sQTLs", "THCA_Survival_sQTLs", "THYM_Survival_sQTLs", "UCEC_Survival_sQTLs", "UCS_Survival_sQTLs", "UVM_Survival_sQTLs", "ACC_GWAS_sQTLs", "BLCA_GWAS_sQTLs", "BRCA_GWAS_sQTLs", "CESC_GWAS_sQTLs", "CHOL_GWAS_sQTLs", "COAD_GWAS_sQTLs", "DLBC_GWAS_sQTLs", "ESCA_GWAS_sQTLs", "GBM_GWAS_sQTLs", "HNSC_GWAS_sQTLs", "KICH_GWAS_sQTLs", "KIRC_GWAS_sQTLs", "KIRP_GWAS_sQTLs", "LAML_GWAS_sQTLs", "LGG_GWAS_sQTLs", "LIHC_GWAS_sQTLs", "LUAD_GWAS_sQTLs", "LUSC_GWAS_sQTLs", "MESO_GWAS_sQTLs", "OV_GWAS_sQTLs", "PAAD_GWAS_sQTLs", "PCPG_GWAS_sQTLs", "PRAD_GWAS_sQTLs", "READ_GWAS_sQTLs", "SARC_GWAS_sQTLs", "SKCM_GWAS_sQTLs", "STAD_GWAS_sQTLs", "TGCT_GWAS_sQTLs", "THCA_GWAS_sQTLs", "THYM_GWAS_sQTLs", "UCEC_GWAS_sQTLs", "UCS_GWAS_sQTLs", "UVM_GWAS_sQTLs"]
+
+[db_pmkb]
+source_url = "https://pmkb.weill.cornell.edu/therapies/download.xlsx"
+version_available = "latest"
+
+[db_sedb]
+source_url = "http://www.licpathway.net/sedb/download/{{version}}"
+version_available = "latest"
diff --git a/inst/extdata/config/db/db_meta.toml b/inst/extdata/config/db/db_meta.toml
@@ -436,3 +436,18 @@ publication = "EWASdb: epigenome-wide association study database. Nucleic Acids
 title = "CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer."
 description = "Alternative splicing (AS) is a widespread process that increases structural transcript variation and proteome diversity. Aberrant splicing patterns are frequently observed in cancer initiation, progress, prognosis and therapy. Increasing evidence has demonstrated that AS events could undergo modulation by genetic variants. The identification of splicing quantitative trait loci (sQTLs), genetic variants that affect AS events, might represent an important step toward fully understanding the contribution of genetic variants in disease development. However, no database has yet been developed to systematically analyze sQTLs across multiple cancer types. Using genotype data from The Cancer Genome Atlas and corresponding AS values calculated by TCGASpliceSeq, we developed a computational pipeline to identify sQTLs from 9 026 tumor samples in 33 cancer types. We totally identified 4 599 598 sQTLs across all cancer types. We further performed survival analyses and identified 17 072 sQTLs associated with patient overall survival times. Furthermore, using genome-wide association study (GWAS) catalog data, we identified 1 180 132 sQTLs overlapping with known GWAS linkage disequilibrium regions. Finally, we constructed a user-friendly database, CancerSplicingQTL (http: //www.cancersplicingqtl-hust.com/) for users to conveniently browse, search and download data of interest. This database provides an informative sQTL resource for further characterizing the potential functional roles of SNPs that control transcript isoforms in human cancer."
 publication = "CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Res. 2018 Oct 17. doi: 10.1093/nar/gky954."
+
+[db.item.pmkb]
+title = "The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations."
+description = """
+OBJECTIVE:
+This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu ), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations.
+MATERIALS AND METHODS:
+PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically.
+RESULTS:
+At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB's interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API.
+DISCUSSION:
+An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology.
+CONCLUSION:
+The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API."""
+publication = "The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations. J Am Med Inform Assoc. 2017 May 1;24(3):513-519. doi: 10.1093/jamia/ocw148 (IF: 4.27)."