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ChangeLog
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2019-05-12 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* migrated Shiny application
2018-10-10 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* major change (for latest RcppTOML) in database.toml and
related parameters name (. => _)
2018-09-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* fix cran check error
2018-06-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* update input UI when upload and delete files
2018-06-01 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add pipeline tabitem
2018-05-31 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* Update Dockerfile and fix websocket connection
* Opencpu package REST API
2018-05-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* fix download.database warning message (newest ini)
2018-05-23 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* support download/preview function for upload/output files
2018-05-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* Support annotation module in shiny
2018-05-21 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* Annotation tabitem UI
* shiny tableout to DT tableout
* vcfanno, vep, annovar change cmd 'print' to message
* set solidHeader = FALSE in shiny box
* add upload filetypes
* improve input UI render method (render_input_box_ui)
2018-05-20 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* support background workers to process long time R commands
* support clusterProfiler
* auto update system monitor in dashbord page (10s)
2018-05-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add dashbord page in shiny app
2018-05-17 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add function check_shiny_dep
* tryCatch for shiny app commands
2018-05-15 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* shiny APP support maftools demo plot with update function
2018-05-08 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* delete upload items supported in shiny APP
2018-05-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add 2018sih_wgs_nkt_full_sqlite in normal pool
2018-02-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* initial anor shiny App (inst/extdata/tools/shiny)
2018-01-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* improve download.database for single
download.name and multiple version
* add docm, intogen, disgenet and cancer_hotspots
databases support
2018-01-18 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add returned colnames test
2018-01-17 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* fix a check bug in annovar
2018-01-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* R/annotation.R annotation.cols.match and
annotation.region.match added parameter fread.db.params
2018-01-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* added mysql.auto.build and mysql.auto.index
* supported external tools vep and vcfanno
* use vcfR package to parse VCF files to data.table object
2017-12-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* modified in dependence
* change download.database parameters order
2017-12-15 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* if os is windows set annovar.dir in PATH
* use annovar.anno.names when anno.name equal perl_annovar_merge
* download.database support multiple download.name
* improve test coverage
2017-12-14 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* fix testthat 2.0 check error
2017-12-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* use ANNOVAR to annotate R object and input.file
* dbscsnv11 be supported
* add nastring paramter in annovar
2017-12-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add tall_somatic_genes_201706
2017-12-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* add set.db.sync.version and set.table.sync.version to get db and
table name (R/external_function.R)
2017-12-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* fix start_index length error
* when skip != 0, the header set FALSE in fread (sqlite.auto.build)
* return.col.names.profix be support
2017-12-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* optimize sqlite.auto.build
* add func get.annotation.needcols in R/get.R
* add param overwrite and append in sqlite.auto.build
2017-12-02 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* download.database use default version
* update function annovar document
* download.database use download.name and download.cfg
* add function get.download.name
* dbname.fixed and table.name.fixed can be used in database.cfg
* new database be supoorted
* set function parameters default value
2017-11-30 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* b_all_rnaseq_v1_core and b_all_rnaseq_v1_extra be added
2017-11-29 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* hgnc_coding_gene2pre and hgnc_coding_pre2gene be supported
* not show warnings in fread database step
2017-11-27 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* use do.call process external function
* document re-format
* convert2annovar.pl be added in annovar
2017-11-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* sqlite.auto.build use split_row_file to
process big file
* vignettes be added
2017-11-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* Function annovar be added in R/external_tools.R
2017-11-23 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* CSCD database be supported
* region match full tested
* epi_genes_v1 be supported
2017-11-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* Parallel and big.file mode be extract
2017-06-08 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* Download .sql file and convert to sqlite automatically
2017-06-07 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* sql2sqlite be added in R/build.R
2017-06-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* finished file check step be added
2017-06-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* MySQL db.type be supported
* build database from a file or a data.table object (R/build.R)
* dbname.fixed and table.name.fixed be added (R/annotation.R)
2017-06-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>
* ANNOVAR databases download full supported
* download.database use buildver
* Unit test of download.database