文章 NCBI批量下载数据,省时又省力

...db=args.database, term=args.term, idtype="acc")record = Entrez.read(handle)for i in record['IdList']:    print i+'\n'    handle = Entrez.efetch(db=args.database, id=i, rettype=args.rettype, retmode="text")    #print(handle.read())    record = SeqIO.read(handle, args.rettype)    SeqIO.write...

文章 细胞焦亡、铁死亡及铜死亡等基因集

...因：    Autophagy-associated genes (relevance score > 4) were retrieved at the GeneCards website (https://www.genecards.org/) by searching the term “autophagy.”  A total of 1,287 ARGs were acquired from the Human Autophagy Database (HADb; http://autophagy.lu/clustering/index.html)...

文章 肠道微生物诊断慢性肾病-随机森林分析文献复现 IF=15分文章

... 25.10 1 6.7 5 156.0 172 0.39 1.11 6.1 314## SRR10028939 female 24.17 0 6.7 2.99 89.0 164 1.10 2.81 33.9 687## SRR10028938 male 23.68 0 66 4.89 132.0 249 1.00 0.74 5.3 263## SRR10028937 male 23.18 1 8.71 5.04 149.3 242 0.78 1.09 11.3 ...

文章 R-对NA 数据进行处理

... 7 10D 4 9 1 将所有空值用0代替 > for(i in 1:ncol(dat)){+ dat[is.na(dat[,i]),i]=0+}> dat sample1 sample2 sample2.1A 1 5 8B 2 0 0C 0 7 10D 4 9 1 删除所有的NA数据 > f...

话题 which

文章 ANNOVAR人类各个数据库变异注释结果表格说明

...eterious; T: Tolerated VEST3_score Variant effect scoring tool；Random forest classifier， higher values are more deleterious CADD_raw CADD raw score CADD_phred CADD phred-like score，higher values are more deleterious GERP++_RS GREP++ "rejected substitutions" (RS) score，higher sc...

问题 GEO数据库下载的表达矩阵转换成genesymbol。

...p($exp);my @samp1e=(localtime(time));if($.==1){my @expArr=split(/\t/,$exp);for(my $i=0;$i<=$#expArr;$i++){my $singleName=$expArr[$i];$singleName=~s/\"//g;if($i==0){push(@sampleName,"ID_REF");}else{my @singleArr=split(/\_|\./,$singleName);push(@sampleName,$singleArr[0]);}}}else{my @expArr=split(/\...

问题 安装ggpubr 报错

ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/peter/R/x86_64-pc-linux-gnu-library/3.4/nloptr’ ERROR: dependency ‘nloptr’ is not available for package ‘lme4’ * removing ‘/home/peter/R/x86_64-pc-linux-gnu-library/3.4/lme4’ libtool: link: ERROR: no informatio...

问题 meme分析后显示error at: maxw

...gt; [optional arguments]<dataset> file containing sequences in FASTA format[-h]print this message[-o <output dir>]name of directory for output fileswill not replace existing directory[-oc <output dir>]name of directory for output fileswill replace existing directory[-text]output in...

文章 根据fastq ID列表，输出指定ID对应的双端或单端fastq文件

...> 'linear'}); $progress->minor(0); # Disabling minor updates for better performance my $count = 0; while (my $seq_obj = $fq_in->next_seq()) { my $id = $seq_obj->id; my ($cleaned_id) = $id =~ /([^@]+)/; # 移除 "@" 符号 if (exists $keep_ref->{$...

问题 R包安装错误 cp: cannot stat ‘hdf5/src/.libs/libhdf5.a’: No such file or directory make: *** [copying] Error 1 ERROR: compilation failed for package ‘Rhdf5lib’

... file or directory make: *** [copying] Error 1 ERROR: compilation failed for package ‘Rhdf5lib’ * removing ‘/share/work/biosoft/R/R-v4.0.3/lib64/R/library/Rhdf5lib’ * installing *source* package ‘BiocStyle’ ... ** using staged installation ** R

问题 braker报错

...t find environment variable $AUGUSTUS_BIN_PATH (either variable does not exist, or the path given in variable does not exist). Will try to set this variable in a different way, later. # Tue Jan 16 17:02:31 2024: Trying to guess $AUGUSTUS_BIN_PATH from $AUGUSTUS_CONFIG_PATH. # Tue Jan 16 17:02:31 2...

问题 关于annover建库问题

... CMD: gtfToGenePred -genePredExt peargff.gtf unknown_refGene.txt RUN CMD: retrieve_seq_from_fasta.pl --format refGene --seqfile pearref.fa  unknown_refGene.txt --out unknown_refGeneMrna.fa NOTICE: Reading region file unknown_refGene.txt ... Done with 56553 regions from 17 chromosomes NOTICE: Fin...

文章 ssh登陆报错

...!It is also possible that a host key has just been changed.The fingerprint for the ECDSA key sent by the remote host isSHA256:XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.Please contact your system administrator.Add correct host key in /home/user01/.ssh/known_hosts to get rid of this message.Offending...

文章 perl 中 $#ARGV 是什么意思

...档说明： The array @ARGV contains the command-line arguments intended for the script. $#ARGV is generally the number of arguments minus one, because $ARGV[0] is the first argument, not the program's command name itself. See $0 for the command name. $#加数组名表示数组最后一个元素...