文章 MFP - Molecular Functional Portrait

...e ore more metrics.best_threshold = '0.51'#best_threshold = 0.51def detect_type(ser, scores):    #cmeans = pd.DataFrame({cg: scores.loc[samps.index].mean() for cg, samps in ser.groupby(ser)})    cmeans = pd.DataFrame({cg: scores.loc[samps.index].mean() for cg, samps in ser.groupby("group")})  ...

文章 生命大数据

... Yuankun Zhu   Bioinformatics Engineer Supervisor   The Children's Hospital Of Philadelphia   7 Changqing Zeng   Professor   Chinese Academy of Sciences   8 陈钢   CEO   微基因   9 ...

文章 微生物多样性16S计算物种累计曲线

...ethod = "random") png(file="spe.png",h=2000,w=2000,res=300) plot(all, ci.type = "poly", col = "blue", lwd = 2, ci.lty = 0, ci.col = "lightblue", main = "Species Accumulation Curves", xlab = "Number of samples", ylab = "Number of species") boxplot(all, col = "yellow", add = TRUE, pch = "+"...

问题 Rstudio server 报错可能原因，重启 服务器之后

2024-10-16T04:36:29.877113Z [rserver] ERROR Unable to determine real path of R script /share/biosoft/R/latest/bin/R (system error 13 (Permission denied)); LOGGED FROM: bool rstudio::core::r_util::{anonymous}::validateRScriptPath(const string&, std::string*) src/cpp/core/r_util/REnvironmentPosix....

用户 what a big fish

问题 ANNOVAR变异注释报错：Erro: invalid record found in exonic_variant_function file (exonic format error)

...l refGene -operation g -nastring . -vcfinput 报错所有信息：NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior) NOTICE: Running with system command <convert2annovar.pl  -includeinfo -allsample -withfreq -format vcf4 /work/bdorsalis/4.snp_indel...

文章 基因家族分析后续试验怎么做？

...含33 TCP家族成员；class II（CIN and CYC/TB1）包含：12个CYC/TB1-type ； 21个CIN-type。 其中比较特殊的TB1在染色体4和染色体5上分别有一个拷贝，并且每个都有3个同源基因（位于A、B、D亚组）；其中染色体4上的TB1已有报道与花序发育有...

问题 用R可视化snp分布的时候出现错误：WARNING: ignoring environment value of R_HOME Fatal error: cannot create 'R_TempDir'

# Rscript $scriptdir/var_density.R -i snp.unknown_multianno.vcf  -b 1000000 -c "darkgreen,yellow,red" -t "SNP Density" WARNING: ignoring environment value of R_HOME Fatal error: cannot create 'R_TempDir'

问题 omicsclass/pan-genome:v1.1镜像OrthoFinder.py报错

运行动植物泛基因组教程02.gene_family.sh命令如下：orthofinder.py -f pep \ -S diamond \ -M msa \ -A muscle \ -T fasttree \ -t 10 \ -a 2 报错如下：Best outgroup(s) for species tree---------------------------------2024-11-15 10:50:56 : Starting STRIDEERROR: Species tree inf...

问题 请问各位老师，WGCNA分析中没有性状数据，但分析了两份基因表达数据，我想要得到Module-module relationships的图，应该怎样修改这部分打的代码呢？

...ait relationships.pdf",width=10,height=6) # Will display correlations and their p-values textMatrix = paste(signif(moduleTraitCor, 2), "\n(",                    signif(moduleTraitPvalue, 1), ")", sep = "") dim(textMatrix) = dim(moduleTraitCor) par(mar = c(6, 8.5, 3, 3)) # Display...

问题 全基因组关联分析GWAS教程中的beagle填充问题

...galArgumentException: Sample Line68 has an inconsistent number of alleles. The first genotype is diploid, but the genotype at position Chr2:35902177 is haploid

文章 BUSCO评估基因组组装和完整性详解

...O评估结果文件。 格式如下： # BUSCO version is: 5.3.2# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)# Summarized benchmarking in BUSCO notation for file /share/nas5/wangq/project/genome_ass...

文章 shuf 随机抽取txt文件的行到新文件 linux命令

...数]...　或者:  shuf -i LO-HI [选项]...Write a random permutation of the input lines to standard output. 如果没有指定文件，或者文件为"-"，则从标准输入读取。 必选参数对长短选项同时适用。  -e, --echo                treat each ARG as an input line...

问题 老师您好，我在做物种间基因组共线性分析时没有得到.anchors文件并且出现list index out of range报错,请问一下是什么原因？

所选的基因组是线粒体基因组测序的结果。

问题 在docker中用cleandata与宿主序列比对得到sam文件这一步出现错误，

...tie.map.log  # Filter and output as SAM(or BAM),-f 4 to Remove reads from the alignment,  # if you want to keep the -F on the alignment (12 for both ends), add -b before the output to output in BAM format samtools view --threads 6 \ -f 12 -h \ $workdir/1.host_del_and_qc/cleandata/${i}.bowtie.sam \...