找到约 15 条结果

文章 read.table参数

... na.strings = "NA", colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = "#", allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAs...

文章 pfam上不去 打开后搜索没有反应

...库一般是可以打开的，但是如果想搜索的话是不行的： Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser. ...

文章 bedtools统计序列中碱基含量

...如下： Tool:    bedtools nuc (aka nucBed)Version: v2.25.0Summary: Profiles the nucleotide content of intervals in a fasta file.Usage:   bedtools nuc [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>Options:        -fi     Input FASTA file        -bed    BED/GFF/VCF file of rang...

问题 进行bugbase运行时候老报错

...us/fastmap.txt  -c loc -o bugbase_loc --> Q&A for bioinformatics, please visit the website: www.omicsclass.com --> Recommended to learn R language:  --> https://study.163.com/course/introduction/1209073807.htm?share=1&shareId=1030291076 [1] "Loading Inputs..." [1] "16S copy n...

文章 下载TCGA临床信息中的用药信息

... <- "Clinical" data_type <- "Clinical Supplement" legacy <- FALSE file_type = "xml" # 设置工作目录 setwd(work_dir) # 下载临床数据的结果 DataDirectory <- paste0(work_dir,"/GDC/",gsub("-","_",project)) # 查询可以下载的数据 query <- GDCquery(project = project, ...

文章 heatmap_group_plot.r 分组热图展示免疫侵润结果

... $ Rscript  heatmap_group_plot.r -husage: heatmap_group_plot.r [-h] -i filepath -m                                                          filepath -g group                                                          [group ...]        ...

文章 库文件位置问题

...    8       9     ellipse     10      11 Error in dyn.load(file, DLLpath = DLLpath, ...) :      12   unable to load shared object '/share/work/biosoft/R/R-v4.2.0/lib64/R/library/units/libs/units.so':     13   libudunits2.so.0: cannot open shared object file: No such file o...

文章 kraken2生成的biom文件处理

...ArgumentParser() parser.add_argument('-i', '--input', help='Input biom file', required=True) parser.add_argument('-o', '--output', help='Output biom file', required=True) args = parser.parse_args() # Load the BIOM table table = load_table(args.input) # Get the OTU IDs and t...

文章 immune_infiltrates_rnaseq.r RNA-seq 转录组数据免疫侵润分析

...ired]  -t type, --type type  TIMER uses indication-specific reference profiles.                        [optional]  --tpm                 whether convert fpkm to tpm [optional, default: False]  -o outdir, --outdir outdir                        output file director...

文章 Bio-Linux中的生物信息学软件

...tilities.bamtools2.4.0+dfsgtoolkit for manipulating BAM (genome alignment) filesbeam20.1+20101008SNP-SNP interaction association mapping based on SNP-block modelsbedtools2.17.0suite of utilities for comparing genomic featuresberkeley-express1.5.1Streaming quantification for high-throughput sequencin...

问题 使用xpclr_smooth_line_plot.r绘制时，没有报错，但没有图片生成

... 19226500  -n all.chr.xpclr.smoothline --> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/ --> R beginners ? I suggest your  learning  R language: https://study.omicsclass.com/index Loading required package: ggplot2 chr_name =  1 chr_name =  8 chr_name =...

文章 tsne_analysis.r 表达聚类分析

...ne_analysis.r -h usage: /work/my_stad_immu/scripts/tsne_analysis.r [-h] -i filepath -m metadata [-d dims] [-p perplexity] [--theta theta] [-M initial_...

问题 reseqv2.0镜像annovar报错

.../5.var_ann/snp.avinput> NOTICE: Finished reading 656047 lines from VCF file NOTICE: A total of 656008 locus in VCF file passed QC threshold, representing 541319 SNPs (375593 transitions and 165726 transversions) and 114689 indels/substitutions NOTICE: Finished writing allele frequencies based ...

问题 NGS数据分析时，使用ANNOVAR的table_annovar.pl报错。

...ariation.pl -geneanno -buildver HP ./bin/M5-31.avinput HPdb/NOTICE: Output files are written to ./bin/M5-31.avinput.variant_function, ./bin/M5-31.avinput.exonic_variant_functionNOTICE: Reading gene annotation from HPdb/HP_refGene.txt ... Done with 1609 transcripts (including 43 without coding sequen...

文章 mclust analysis.r 基于模型的聚类

...t -i gene_data, --gene_data gene_data input data file path[required] -m metadata, --metadata metadata input clinical information file path[required] --mclust whether to cluster the samples[optional,default:False] -g group, --group ...