release v0.3.7

JhuangLab · Nov 20, 2018 · 71b9f61 · 71b9f61
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# BioInstaller 0.3.7
+
+## New features
+
+* support bitbucket repo
+* remove function "check_shiny_dep" use pacman install dependences 
+* add new databases and tools (meta and files)
+
+## Minor bugs fixed
+
+* fix "version\_avaliable" to "version\_available" in ~10 item
+
 # BioInstaller 0.3.6
 
 ## New features

diff --git a/inst/extdata/config/db/db_main.toml b/inst/extdata/config/db/db_main.toml
@@ -455,3 +455,21 @@ version_available = "latest"
 [db_sedb]
 source_url = "http://www.licpathway.net/sedb/download/{{version}}"
 version_available = "latest"
+
+[db_lnc2cancer]
+source_url = "http://www.bio-bigdata.net/lnc2cancer/download/{{version}}.txt"
+version_available = ["all_lnc_cancer_associations", "Circulating_lnc_cancer_associations", "Prognostic_lnc_cancer_associations",
+                     "Drug-resistant_lnc_cancer_associations", "LncRNAs%20regulated%20by%20TF%20in%20cancers",
+                     "LncRNAs%20regulated%20by%20miRNA%20in%20cancers", "LncRNAs%20regulated%20by%20variant%20in%20cancers",
+                     "LncRNAs%20regulated%20by%20methylation%20in%20cancers"]
+
+[db_fusiongdb]
+source_url = "https://ccsm.uth.edu/FusionGDB/tables/{{version}}.txt"
+version_available = ["TCGA_ChiTaRS_combined_fusion_information_on_hg19", "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_fgID",
+                     "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19", "TCGA_ChiTaRS_combined_fusion_Prot_feature_retention_search_UniProt_for_Hgene",
+                     "TCGA_ChiTaRS_combined_fusion_Prot_feature_retention_search_UniProt_for_Tgene", 
+                     "fusion_ppi", "fusion_uniprot_related_drugs", "fgene_disease_associations", 
+                     "uniprot_gsymbol", "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_In-frame_100k_check_aminoacid_seq",
+                     "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_In-frame_100k_check_cds_seq",
+                     "TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19_In-frame_100k_check_transcript_seq",
+                     "In-frame_fgene_num_samples"]
diff --git a/inst/extdata/config/db/db_meta.toml b/inst/extdata/config/db/db_meta.toml
@@ -451,3 +451,13 @@ An accurate and up-to-date knowledge base of genomic alterations of clinical sig
 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)."
+
+[db.item.lnc2cancer]
+title = "Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers"
+description = """Lnc2Cancer 2.0 (http://www.bio-bigdata.net/lnc2cancer) is an updated database that provides comprehensive experimentally supported associations between lncRNAs and human cancers. In Lnc2Cancer 2.0, we have updated the database with more data and several new features, including (i) exceeding a 4-fold increase over the previous version, recruiting 4989 lncRNA-cancer associations between 1614 lncRNAs and 165 cancer subtypes. (ii) newly adding about 800 experimentally supported circulating, drug-resistant and prognostic-related lncRNAs in various cancers. (iii) appending the regulatory mechanism of lncRNA in cancer, including microRNA (miRNA), transcription factor (TF), variant andmethylation regulation. (iv) increasing more than 70 high-throughput experiments (microarray and next-generation sequencing) of lncRNAs in cancers. (v) Scoring the associations between lncRNA and cancer to evaluate the correlations. (vi) updating the annotation information of lncRNAs (version 28) and containing more detailed descriptions for lncRNAs and cancers. Moreover, a newly designed, user-friendly interface was also developed to provide a convenient platform for users. In particular, the functions of browsing data by cancer primary organ, biomarker type and regulatory mechanism, advanced search following several features and filtering the data by LncRNA-Cancer score were enhanced. Lnc2Cancer 2.0 will be a useful resource platform for further understanding the associations between lncRNA and human cancer. """
+publication = "Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1096."
+
+[db.item.fusiongdb]
+title = "FusionGDB: fusion gene annotation DataBase"
+description = """Gene fusion is one of the hallmarks of cancer genome via chromosomal rearrangement initiated by DNA double-strand breakage. To date, many fusion genes (FGs) have been established as important biomarkers and therapeutic targets in multiple cancer types. To better understand the function of FGs in cancer types and to promote the discovery of clinically relevant FGs, we built FusionGDB (Fusion Gene annotation DataBase) available at https://ccsm.uth.edu/FusionGDB. We collected 48 117 FGs across pan-cancer from three representative fusion gene resources: the improved database of chimeric transcripts and RNA-seq data (ChiTaRS 3.1), an integrative resource for cancerassociated transcript fusions (TumorFusions), and The Cancer Genome Atlas (TCGA) fusions by Gao et al. For these ∼48K FGs, we performed functional annotations including gene assessment across pancancer fusion genes, open reading frame (ORF) assignment, and retention search of 39 protein features based on gene structures of multiple isoforms with different breakpoints. We also provided the fusion transcript and amino acid sequences according to multiple breakpoints and transcript isoforms. Our analyses identified 331, 303 and 667 in-frame FGs with retaining kinase, DNA-binding, and epigenetic factor domains, respectively, as well as 976 FGs lost protein-protein interaction. FusionGDB provides six categories of annotations: FusionGeneSummary, FusionProtFeature, FusionGeneSequence, Fusion- GenePPI, RelatedDrug and RelatedDisease."""
+publication = "FusionGDB: fusion gene annotation DataBase. Nucleic Acids Res. 2018 Nov 8. doi: 10.1093/nar/gky1067."
diff --git a/vignettes/BioInstaller.Rmd b/vignettes/BioInstaller.Rmd
@@ -17,7 +17,7 @@ vignette: >
 ---
 
 ```{r, echo = FALSE}
-knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
+knitr::opts_chunk$set(comment = "#>", collapse = TRUE, screenshot.force = FALSE)
 ```
 
 ## Introduction

diff --git a/vignettes/download.Rmd b/vignettes/download.Rmd
@@ -17,7 +17,7 @@ vignette: >
 ---
 
 ```{r, echo = FALSE}
-knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
+knitr::opts_chunk$set(comment = "#>", collapse = TRUE, screenshot.force = FALSE)
 ```
 
 ## Github
@@ -30,6 +30,10 @@ CRAN: https://CRAN.R-project.org/package=BioInstaller
 
 ## JhuangLab host
 
+### BioInstaller 0.3.7
+
+Download [here](http://bioinfo.rjh.com.cn/download/bioinstaller/bioinstaller/v0.3.7.tar.gz).
+
 ### BioInstaller 0.3.6
 
 Download [here](http://bioinfo.rjh.com.cn/download/bioinstaller/bioinstaller/v0.3.6.tar.gz).

diff --git a/vignettes/items_description.Rmd b/vignettes/items_description.Rmd
@@ -17,7 +17,7 @@ vignette: >
 ---
 
 ```{r, echo = FALSE}
-knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
+knitr::opts_chunk$set(comment = "#>", collapse = TRUE, screenshot.force = FALSE)
 get_dt <- function(item) {
   Name <- names(item)
   Description <- unname(unlist(lapply(item, function(x){

diff --git a/vignettes/plugins_of_BioInstaller_shiny.Rmd b/vignettes/plugins_of_BioInstaller_shiny.Rmd
@@ -17,7 +17,7 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(echo = TRUE, screenshot.force = FALSE, comment = "#>", collapse = TRUE)
 ```
 
 ## Introduction

diff --git a/vignettes/start_shiny_of_BioInstaller.Rmd b/vignettes/start_shiny_of_BioInstaller.Rmd
@@ -17,7 +17,7 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(echo = TRUE, screenshot.force = FALSE, comment = "#>", collapse = TRUE)
 ```
 
 ## Introduction

diff --git a/vignettes/write_configuration_file.Rmd b/vignettes/write_configuration_file.Rmd
@@ -17,7 +17,7 @@ vignette: >
 ---
 
 ```{r, echo = FALSE}
-knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
+knitr::opts_chunk$set(comment = "#>", collapse = TRUE, screenshot.force = FALSE)
 ```
 
 Configuration files in BioInstaller are important. We used these configuration files to stored the software and databases URL, the script of installation, and other useful information.