找到约 15 条结果

文章 ANNOVAR琳琅满目的人类变异信息注释数据库

...位置(chromEnd)、名称(name)、染色标识(gieStain)‘1000g2015aug’ for alternative allele frequency in the 1000 Genomes Project 。1000基因组项目(和ExAV 外显子集合联合一样,是公开、开放的数据库)里面供选择的等位基因频率信息。‘exac03’for the var...

问题 WGCNA-MAD

...############ input data########################## # The following setting is important, do not omit. options(stringsAsFactors = FALSE) #读取数据,删除第一列GeneSymbol datExpr = read.table(expr_file,header=T,row.names=1,comment.char = "",check.names=F) datExpr = datExpr[,-1] # Take a ...

文章 RagTag:同源锚定延伸

...   build a FASTA file from an AGP file      agpcheck        check for valid AGP file format      asmstats        assembly statistics      splitasm        split an assembly at gaps      delta2paf       delta to PAF file conversion      paf2delta       PAF to delta ...

问题 genome-annotation的docker转singularity的容器后,rmblast使用报错。

...候出现总线吐核错误。这种情况该怎么办? 其实运行Ltr-Retrieve脚本也有这样的问题,它首先进行测试各个依赖软件的,也是在这块挂掉。后来修改了一下脚本欺骗了一下才通过的。 New DB name:   /share/work/biosoft/RepeatMasker/RepeatMas...

问题 R语言分析GEO数据,您好老师,19年参加培训的时候就是用的R3.6.1,自己运行出现如下报错

...0709cdf' Installation path not writeable, unable to update packages: boot, foreign, KernSmooth, lattice, Matrix, mgcv, nlme, nnet, survival Old packages: 'BH', 'bibtex', 'BiocParallel', 'bit', 'blob', 'broom', 'callr', 'caret', 'caTools', 'checkmate', 'chron', 'cli', 'clusterProfiler', 'data.table...

问题 检查数据是否正确时 出现以下错误:> exprSize = checkSets(multiExpr) Error in checkSets(multiExpr) : data does not appear to have the correct format. Consider using fixDataStructureor setting checkStructure = TRUE when calling this function.

...微信 18289816802 Error in multiExpr[[1]]$data : $ operator is invalid for atomic vectors Error in checkSets(multiExpr) : data does not appear to have the correct format. Consider using fixDataStructureor setting checkStructure = TRUE when calling this function.

文章 python代码到pubmed上搜索关键字,统计每年发文章数量

...l" def search_pubmed(keyword, retmax=10000): print(f"Searching PubMed for '{keyword}'...") handle = Entrez.esearch(db="pubmed", term=keyword, retmax=retmax, datetype="pdat") record = Entrez.read(handle) id_list = record["IdList"] print(f"Found {len(id_list)} articles.") retu...

文章 lasso_cox.r lasso_cox 模型优化分析

...iate ...], --variate variate [variate ...] variate for cox analysis [required] -s seed, --seed seed set random seed [default 2021] -l lambda, --lambda lambda set lambda cut off [default NULL] -P predict.time, --predict.time predict.time ...

文章 clusterProfiler做非模式物种的功能注释

... rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["AH10561"]]' title AH10561 | hom.Oryza_sativa.inp8.sqlite AH59059 | org.Oryza_sativa_Japonica_Group.eg.sqlite 需要注...

文章 Infercnv|单细胞转录组拷贝数分析

... [-t type] -g group [group ...] [--platform platform] [--hmm] [-o path] single cell trajectory analysis : http://cole-trapnell-lab.github.io/monocle- release/docs/#constructing-single-cell-trajectories optional arguments: -h, --help show this help m...

文章 单拷贝直系同源基因构建系统发育树以及分歧时间

...ed by MAFFT v7.158b [74] software, and were combined into a long sequence for each species. Then, the conserved block regions of the alignment were picked out by Gblocks 0.91b with default parameters [75] of the software, and the final alignment length was 193323 aa. With the input of this align...

问题 老师好,我想问一下,RSEM、FPKM和TPM是一个什么样的关系呢?reads count又有怎样的用途,与前面三个有关系吗?有一篇paper中说,The RNA-Seq by Expectation–Maximization (RSEM) expression values were used for statistical analysis.这是说统计学分析需要用RSEM标准化处理后才能进行吗?

问题 基因家族分析时,提取cds与pep序列报错

...错如下,数据来源:ncbi的参考基因组注释文件。 /share/work/biosoft/TransDecoder/latest/util/gff3_file_to_proteins.pl --gff3 $species.longest_isoform.gff3 --fasta $genome --seqType CDS >$species.cds.fa#提取pep序列/share/work/biosoft/TransDecoder/latest/util/gff3_file_to_p...

问题 不能使用scripts中的vcf2map.pl脚本

...-Md 10 -o pop.genotype.gz该命令运行后显示Can't open perl script "/work/scripts//vcf2map.pl": No such file or directory 切换到scripts中授权chmod a+x vcf2map.pl后再回到01.PrepareData运行上述命令还是不行 使用绝对路径 perl /work/scripts//vcf2map.pl -i ../00.DataQC/al...

文章 echo输出不换行

...echo命令的-n选项,作用是输出是不追加换行。 #!/bin/bash/for i in `cat sample.txt`do        echo -n "cat ">> run.sh        for j in `cat primerid.txt`        do                echo -n " $i/${i}_$j.fa">> run.sh        done        echo  "> $...