1时间轴的情节

该文件只包含五年期间产生的最重要数据的一个子集。中所有注释示例(S)和工作单元(W)的概述，以获得印象B-Fabric系统,Türker et al. (2010)，在时间轴图中。

NGS数据p1644

质谱仪数据p1875

2生成数据(替换使数据。R）

NL42_100K <- NestLink:::.getReadsFromFastq("inst/extdata/NL42_100K.fastq.gz") save(NL42_100K, file="inst/extdata/NestLink_NL42_100K.RData")

expFile <- query(eh, c("NestLink"， "NL42_100K.fastq.gz"))[[1]] expect_true(file.exists(expFile)) scratchFolder <- tempdir() setwd(scratchFolder) knownNB_File <- query(eh, c("NestLink"， "knownNB.txt"))[[1]] knownNB_data <- read。table(knownNB_File, sep='\t'， header = TRUE, row.names = 1, stringsAsFactors = FALSE) knownNB <- Biostrings::translate(DNAStringSet(knownNB_data$Sequence)) names(knownNB) <- rownames(knownNB_data) knownNB <- sapply(knownNB，toString)参数< -列表()参数[[' NB_Linker1 ']] < -“GGCCggcggGGCC”参数[[' NB_Linker2 ']] < -“GCAGGAGGA”参数[[' ProteaseSite ']] < -“TTAGTCCCAAGA”参数[[' FC_Linker ']] < -“GGCCaaggaggcCGG”参数[[' knownNB ']] < - knownNB参数[[' nReads ']] < - 100参数[[' minRelBestHitFreq ']] < - 0.8参数[[' minConsensusScore ']] < - 0.9参数[[' maxMismatch ']] < - 1参数[[' minNanobodyLength ']] < - 348参数[[' minFlycodeLength ']] < - 33参数[[' FCminFreq ']] < - 1 nanobodyFlycodeLinkage。RData <- runNGSAnalysis(file = expFile[1]， param)

library(stlink) NB <- gettnb () FC <- getFC()

load("~/Downloads/444589.RData") library(protViz) library(NestLink) WU160118 <-call('rbind'， lapply(list("F255737"， "F255744"， "F255747"， "F255749"， "F255751"， "F255760"， "F255761"， "F255762")， function(datfilename){df <- as.data.frame.mascot(get(datfilename)) df$datfilename <- datfilename df})) save(WU160118, file = "../inst/extdata/WU160118. "RData"， compress = TRUE, compression_level = 9)

library(ExperimentHub) eh <- ExperimentHub();load(query(eh, c("NestLink"， " wu16118 . rdata "))[[1]]))类(WU160118)

## [1] "data.frame"

PATTERN <- "^GS[ASTNQDEFVLYWGP]{7}(WR|WLTVR|WQEGGR|WLR|WQSR)$" idx <- grepl(PATTERN, WU160118$pep_seq) WU <- WU160118[idx & WU160118$pep_score > 25，]

3.上传至S3

# !/bin/bash aws——profile AnnotationContributor s3 cp NestLink/F255744。RData s3: / / annotation-contributor / NestLink / F255744。RData--acl public-read aws --profile AnnotationContributor s3 cp NestLink/WU160118.RData s3://annotation-contributor/NestLink/WU160118.RData --acl public-read aws --profile AnnotationContributor s3 cp NestLink s3://annotation-contributor/NestLink --recursive --acl public-read

4概述/开始使用BioconductorExperimentHub

加载元数据

Fl <- system。file("extdata"， "metadata.csv"， package='NestLink') kable(metadata <- read.csv(fl, stringsAsFactors=FALSE))

查询和加载NestLink从aws s3打包数据

library(ExperimentHub) eh <- ExperimentHub();查询(呃,“NestLink”)

## # snapshotDate(): 2022-10-24 ## # $dataprovider:功能基因组学中心苏黎世(FGCZ) ## # $species: NA ## # $rdataclass: data.frame, DNAStringSet ## #附加mcols():分类名称，基因组，描述，## # coordinate_1_based，维护者，rdatadateadded，准备类，标签，## # rdatapath, sourceurl, sourcetype ## #检索记录，例如，'对象[["EH2063]]]' ## ##标题## EH2063 |样本NGS NB FC链接数据## EH2064 | Flycodes tryptic消化## EH2065 |纳米体tryptic消化## EH2066 | FASTA作为单元测试的真实基础## EH2067 |已知纳米体## EH2068 | SMEG和COLI的定量结果## EH2069 | F255744吉祥物搜索结果## EH2070 | WU160118吉祥物搜索结果

load(query(eh, c("NestLink"， "F255744. rdata "))[[1]]) dim(F255744)

## [1] 15655 21

load(query(eh, c("NestLink"， "WU160118. rdata "))[[1]])

## [1] 128390 22

5会话信息

下面是编译后的输出sessionInfo ()：

## R版本4.2.1(2022-06-23)##平台:x86_64-pc-linux-gnu(64位)##运行在Ubuntu 20.04.5 LTS ## ##矩阵产品:默认## BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas。/home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack。所以## ## locale: ## [1] LC_CTYPE=en_US。UTF-8 LC_NUMERIC= c# # [3] LC_TIME=en_GB LC_COLLATE= c# # [5] LC_MONETARY=en_US。utf - 8 LC_MESSAGES = en_US。UTF-8 ## [7] LC_PAPER=en_US。UTF-8 LC_NAME= c# # [9] LC_ADDRESS=C lc_phone = c# # [11] LC_MEASUREMENT=en_US。UTF-8 LC_IDENTIFICATION=C ## ##附加的基本包:## [1]stats4 stats graphics grDevices utils datasets methods ##[8]基础## ##其他附加包:# # # # [1] knitr_1.40 scales_1.2.1 [3] ggplot2_3.3.6 NestLink_1.14.0 # # [5] ShortRead_1.56.0 GenomicAlignments_1.34.0 # # [7] SummarizedExperiment_1.28.0 Biobase_2.58.0 # # [9] MatrixGenerics_1.10.0 matrixStats_0.62.0 # # [11] Rsamtools_2.14.0 GenomicRanges_1.50.0 # # [13] BiocParallel_1.32.0 protViz_0.7.3 # # [15] gplots_3.1.3 Biostrings_2.66.0 # # [17] GenomeInfoDb_1.34.0 XVector_0.38.0 # # [19] IRanges_2.32.0 S4Vectors_0.36.0 # # [21] ExperimentHub_2.6.0 AnnotationHub_3.6.0 # # [23] BiocFileCache_2.6.0dbplyr_2.2.1 ## [25] BiocGenerics_0.44.0 BiocStyle_2.26.0 ## ## loaded via a namespace (and not attached): ## [1] nlme_3.1-160 bitops_1.0-7 ## [3] bit64_4.0.5 RColorBrewer_1.1-3 ## [5] filelock_1.0.2 httr_1.4.4 ## [7] tools_4.2.1 bslib_0.4.0 ## [9] utf8_1.2.2 R6_2.5.1 ## [11] KernSmooth_2.23-20 mgcv_1.8-41 ## [13] colorspace_2.0-3 DBI_1.1.3 ## [15] withr_2.5.0 tidyselect_1.2.0 ## [17] bit_4.0.4 curl_4.3.3 ## [19] compiler_4.2.1 cli_3.4.1 ## [21] DelayedArray_0.24.0 labeling_0.4.2 ## [23] bookdown_0.29 sass_0.4.2 ## [25] caTools_1.18.2 rappdirs_0.3.3 ## [27] stringr_1.4.1 digest_0.6.30 ## [29] rmarkdown_2.17 jpeg_0.1-9 ## [31] pkgconfig_2.0.3 htmltools_0.5.3 ## [33] highr_0.9 fastmap_1.1.0 ## [35] rlang_1.0.6 RSQLite_2.2.18 ## [37] shiny_1.7.3 farver_2.1.1 ## [39] jquerylib_0.1.4 generics_0.1.3 ## [41] hwriter_1.3.2.1 jsonlite_1.8.3 ## [43] gtools_3.9.3 dplyr_1.0.10 ## [45] RCurl_1.98-1.9 magrittr_2.0.3 ## [47] GenomeInfoDbData_1.2.9 interp_1.1-3 ## [49] Matrix_1.5-1 munsell_0.5.0 ## [51] Rcpp_1.0.9 fansi_1.0.3 ## [53] lifecycle_1.0.3 stringi_1.7.8 ## [55] yaml_2.3.6 zlibbioc_1.44.0 ## [57] grid_4.2.1 blob_1.2.3 ## [59] parallel_4.2.1 promises_1.2.0.1 ## [61] crayon_1.5.2 deldir_1.0-6 ## [63] lattice_0.20-45 splines_4.2.1 ## [65] KEGGREST_1.38.0 magick_2.7.3 ## [67] pillar_1.8.1 codetools_0.2-18 ## [69] glue_1.6.2 BiocVersion_3.16.0 ## [71] evaluate_0.17 latticeExtra_0.6-30 ## [73] BiocManager_1.30.19 png_0.1-7 ## [75] vctrs_0.5.0 httpuv_1.6.6 ## [77] purrr_0.3.5 gtable_0.3.1 ## [79] assertthat_0.2.1 cachem_1.0.6 ## [81] xfun_0.34 mime_0.12 ## [83] xtable_1.8-4 later_1.3.0 ## [85] tibble_3.1.8 AnnotationDbi_1.60.0 ## [87] memoise_2.0.1 ellipsis_0.3.2 ## [89] interactiveDisplayBase_1.36.0