文章 群体遗传进化与GWAS分析动植物文献

...n W,Xinyue S,Xin J, et al. Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study[J]. Plant Biotechnology Journal.2021.单倍型( haplotype )是共存于单条染色体上的一系列遗传变异位点的组合，其在染色体上形...

问题 误: 无法分配大小为7.4 Mb的矢量 Killed after 9 m

...lation" > platform <- "Illumina Human Methylation 450" > sample_type <- "Primary solid Tumor"    > legacy <- FALSE > # 工作目录如果不存在，则创建目录 > if( !file.exists(work_dir) ){ +   if( !dir.create(work_dir, showWarnings = FALSE, recursive = TRUE)...

文章 immune_bar_plot.r 免疫侵润分析bar绘图

...                        input legend tittle name [default cell type]  -a xlab, --xlab xlab  input xlab [default sample]  -b ylab, --ylab ylab  input ylab [default fraction]  -m metadata, --metadata metadata                        input metadata file [default NULL]  -g g...

文章 seurat_sc_cluster.r 使用帮助：

...ation to run. Can be uwot:Runs umap via                        the uwot R package; uwot-learn:Runs umap via the uwot                        R package and return the learned umap model;umap-                        learn:Run the Seurat wrapper of the python umap-lea...

问题 使用NCBI下载的基因组和gff文件进行基因家族分析时，保留编码蛋白基因的命令似乎无法识别NCBI的gff文件（描述中为日志，图片为尝试获取的gff文件）

...t_sp_filter_feature_by_attribute_value.pl --gff  $gff --attribute gene_biotype --value protein_coding -t '!' -o $species.protein_coding.gff3 Using standard /share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/auto/share/dist/AGAT/config.yaml file 07/31/2024 at 13h07m54s usage: /share/work/b...

文章 R安装units包报错解决方法

...yeschecking for stdlib.h... yeschecking for string.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for strings.h... yeschecking for sys/stat.h... yeschecking for sys/types.h... yeschecking for unistd.h... yeschecking for _Bool... nochecking for stdbool.h that conforms to C...

问题 使用ensembl下载的人gff3文件进行基因家族分析时，保留编码蛋白基因的命令无法识别人的gff3文件（描述中为日志）

...# agat_sp_filter_feature_by_attribute_value.pl --gff  $gff --attribute biotype --value protein_coding -t '!' -o $species.protein_coding.gff3 Using standard /share/work/biosoft/perl/perl-5.22.1/lib/site_perl/5.22.1/auto/share/dist/AGAT/config.yaml file 08/01/2024 at 10h36m50s usage: /share/work/b...

问题 使用xpclr分析出现TypeError: ufunc 'true_divide' not supported for the input types'

...da3/lib/python3.7/site-packages/allel/io/vcf_read.py:1454: UserWarning: no type for field 'variants/None', assuming object   warnings.warn('no type for field %r, assuming %s' % (f, normed_types[f])) /public/home/weijiehong/miniconda3/lib/python3.7/site-packages/allel/io/vcf_read.py:1048: UserWarn...

问题 是没有gene-family了嘛

PS C:\Users\Administrator> docker pull omicsclass/gene-family:v1.0.1 What's next:     View a summary of image vulnerabilities and recommendations → docker scout quickview omicsclass/gene-family:v1.0.1 Error response from daemon: pull access denied for omicsclass/gene-family, repository d...

文章 文本去重并统计重复次数

...ello World. Apple and Nokia. Hello World. I wanna buy an Apple device. The Iphone of Apple company. Hello World. The Iphone of Apple company. My name is Friendfish. Hello World. Apple and Nokia. 命令如下：$ sort test.txt | uniq -c | sort -rn 4 Hello World. 2 The Iphone of Apple comp...

文章 基因家族的定义和形成方式（加倍与扩张）

...上，形成一个序列相似、功能相近的基因簇。According to the descriptions of Holub [1], a chromosomal region within 200 kb containing two or more genes is defined as a tandem duplication event.3.染色体片段复制(Segmental duplication)：导致复制的基因距离较远，甚至...

文章 GOChord_plot.r GOplot包绘制GO弦图

...O_data GO_DATA input a GO enrichment analysis data,the data with columns for 'category','ID','term',adjusted p-value('adj_pval') and 'genes'[required] -d DEG_DATA, --deg_data DEG_DATA input the result o...

文章 HMMER ——hmmsearch 用法，参数

...lled profile hidden Markov models (profile HMMs). HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query ...

问题 fastqc质控时报错，提示Ran out of data in the middle of a fastq entry.是什么问题？

文章 bedtools统计序列中碱基含量

...： 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 ranges to ...