坐山雕 - 博客园

Find all zero-byte files in directory and subdirectories

摘要： find "./" -size 0 阅读全文

posted @ 2021-03-31 15:53 坐山雕阅读(39) 评论(0) 推荐(0)

grep in python

摘要： for line in file: if re.search(pattern, line): print(line) 阅读全文

posted @ 2021-03-30 17:04 坐山雕阅读(45) 评论(0) 推荐(0)

How do I know the script file name in a Bash script?

摘要： me=`basename "$0"` 阅读全文

posted @ 2021-03-30 16:50 坐山雕阅读(44) 评论(0) 推荐(0)

ENCODE Chromatin State Segmentation by HMM from Broad Institute, MIT and MGH

摘要： https://hgsv.washington.edu/cgi-bin/hgFileUi?db=hg38&g=wgEncodeBroadHmm Display Conventions and Configuration This track is a composite track that con 阅读全文

posted @ 2021-03-29 12:46 坐山雕阅读(110) 评论(0) 推荐(0)

macOS cannot verify that this app is free from malware. 怎么解决显示全部

摘要：你比较确定不是恶意软件的情况下，苹果官方给出的解决方案在 Mac 上安全地打开应用是按住Control键点按应用, 然后打开，这样会把应用增加到白名单中许可执行。对于开发者来说，比较简单的办法就是禁用Gatekeeper，执行如下命令：$ sudo spctl --master-disable 作者阅读全文

posted @ 2021-03-28 20:54 坐山雕阅读(3257) 评论(0) 推荐(0)

win10怎么设置游戏录制时间

摘要： https://jingyan.baidu.com/article/ca2d939d50c538eb6c31ce3e.html 阅读全文

posted @ 2021-03-26 14:54 坐山雕阅读(110) 评论(0) 推荐(0)

diy zotero

摘要： https://blog.csdn.net/weixin_41457494/article/details/103967939 https://editor.citationstyles.org/visualEditor/ 阅读全文

posted @ 2021-03-04 19:21 坐山雕阅读(60) 评论(0) 推荐(0)

怎样去掉word中的换行符

摘要： word --> reference --> view --> Show non-Printing Characters --> All --> un-select 阅读全文

posted @ 2021-02-19 17:39 坐山雕阅读(168) 评论(0) 推荐(0)

warning [escuelaslinux6.12-english-64bits.zip]: zipfile claims to be last disk of a multi-part archive;

摘要： simon@ZhengmzLAB:/media/simon/HDD5$ unzip escuelaslinux6.12-english-64bits.zip Archive: escuelaslinux6.12-english-64bits.zip warning [escuelaslinux6.1 阅读全文

posted @ 2021-02-17 20:09 坐山雕阅读(980) 评论(0) 推荐(0)

语音识别: DeepSpeech2

摘要： https://github.com/PaddlePaddle/DeepSpeech/blob/develop/README_cn.md http://proceedings.mlr.press/v48/amodei16.pdf 阅读全文

posted @ 2021-02-17 16:41 坐山雕阅读(774) 评论(0) 推荐(0)

RNA-seq

摘要： STAR 处理后的RNA-seq数据 BAM和bedgraph 在q30和picard后上传的效果一样 scRNAseq也需要split R2上传阅读全文

posted @ 2021-02-16 15:04 坐山雕阅读(248) 评论(0) 推荐(0)

BASIC get track name

摘要： /usr/local/BASIC/_py/bin/python /usr/local/BASIC/basic/console/track_util.py list|grep $F 阅读全文

posted @ 2021-02-16 11:36 坐山雕阅读(47) 评论(0) 推荐(0)

修改 bam 文件中染色体名 add chr

摘要： $1=xxx.bam $2=xxx.chr.bam samtools view -H $1 | sed -e 's/SN:/SN:chr/g' | samtools reheader - $1 > $2 阅读全文

posted @ 2021-02-15 20:24 坐山雕阅读(933) 评论(0) 推荐(0)

conda tophat STAR

摘要： conda create -n tophat python = 2.7 conda install -c bioconda tophat conda install bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the- 阅读全文

posted @ 2021-02-15 11:12 坐山雕阅读(112) 评论(0) 推荐(0)

STARsolo

摘要： you can concatenate the files, or supply them as two (for Read2(barcode) and Read1(cDNA)) comma-separated lists, i.e. Hi Olga, I have finally finished 阅读全文

posted @ 2021-02-14 21:24 坐山雕阅读(344) 评论(0) 推荐(0)

picard

摘要： https://gatk.broadinstitute.org/hc/en-us/articles/360037225972-MarkDuplicates-Picard- 阅读全文

posted @ 2021-02-14 19:46 坐山雕阅读(44) 评论(0) 推荐(0)

STAR

摘要： https://github.com/alexdobin/STAR/issues/175 阅读全文

posted @ 2021-02-13 13:10 坐山雕阅读(29) 评论(0) 推荐(0)

SRR1957059

摘要： https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1957059 https://www.ncbi.nlm.nih.gov/sra?term=SRX982548 https://www.ncbi.nlm.nih.gov/geo/query/acc.c 阅读全文

posted @ 2021-02-09 15:53 坐山雕阅读(71) 评论(0) 推荐(0)

shinyapps.io publish

摘要： https://docs.rstudio.com/shinyapps.io/getting-started.html#installation 阅读全文

posted @ 2021-02-09 15:02 坐山雕阅读(59) 评论(0) 推荐(0)

A Helpful Way to Install R Packages Hosted on GitHub

摘要： https://cran.r-project.org/web/packages/githubinstall/vignettes/githubinstall.html 阅读全文

posted @ 2021-02-09 12:16 坐山雕阅读(43) 评论(0) 推荐(0)

Combine part of a PDF with another PDF in preview in mac

摘要： Combine part of a PDF with another PDF Open the PDFs that you want to combine in Preview. In each document, choose View > Thumbnails to show page thum 阅读全文

posted @ 2021-02-08 11:14 坐山雕阅读(41) 评论(0) 推荐(0)

sshfs mac

摘要： brew install --cask osxfuse brew install sshfs mkdir HDD6 sshfs -p 1911 simon@10.20.1.138:/media/simon/HDD6 HDD6 阅读全文

posted @ 2021-02-03 10:41 坐山雕阅读(60) 评论(0) 推荐(0)

rsync+ssh同步备份文件

摘要： jakqigle 2015-06-13 22:50:50 3532 收藏分类专栏： Linux Software&Tools 文章标签： rsync ssh 版权定期对web代码或重要的文件做同步异地服务器备份，防止服务器故障严重磁盘损坏时文件丢失的问题。备份服务器：192.168.200.1 阅读全文

posted @ 2021-02-02 15:28 坐山雕阅读(135) 评论(0) 推荐(0)

mouse click shiny

摘要： library(ggplot2) ui <- basicPage( plotOutput("plot1", click = "plot_click"), verbatimTextOutput("info") ) server <- function(input, output) { output$p 阅读全文

posted @ 2021-02-01 16:59 坐山雕阅读(43) 评论(0) 推荐(0)

ggplot log2

摘要： PSELC+ scale_y_continuous(trans = log2_trans()) 阅读全文

posted @ 2021-02-01 11:47 坐山雕阅读(42) 评论(0) 推荐(0)

R语言可视化学习笔记之ggridges包. crossed coverage

摘要： https://blog.csdn.net/woodcorpse/article/details/106554057 library(viridis) library(ggridges) head(lincoln_weather[ ,1:4]) ggplot(lincoln_weather, aes 阅读全文

posted @ 2021-02-01 11:04 坐山雕阅读(227) 评论(1) 推荐(0)

white no line rectGrob

摘要： rectGrob(gp=gpar(fill=NA,col=NA)), #Plot Footer my_g1 ← grobTree(rectGrob(gp=gpar(fill="#F0F0F0",col=NA)), linesGrob(unit(c(.05, .95), "npc"), unit(1, 阅读全文

posted @ 2021-02-01 10:29 坐山雕阅读(49) 评论(0) 推荐(0)

R plot a table

摘要： PLOTINFO<-ggplot(SMDATA,aes(x=xorder))+ geom_text(aes(y=3,label=xorder),angle=270)+ geom_text(aes(y=1,label=GENENAME),angle=270)+ geom_text(aes(y=2,la 阅读全文

posted @ 2021-01-26 11:54 坐山雕阅读(71) 评论(0) 推荐(0)

arrangeGrob

摘要： grid.arrange(PLOTKMK$gtable,arrangeGrob(PLOTLINE,PLOTINFO,ncol=1,heights=c(3,1)),ncol=1) 阅读全文

posted @ 2021-01-26 11:43 坐山雕阅读(87) 评论(0) 推荐(0)

sorted a data.frame i colnames

摘要： FIN2 %>% select(sort(names(.))) %>% FIN3 阅读全文

posted @ 2021-01-26 10:41 坐山雕阅读(40) 评论(0) 推荐(0)

R list chr to integer

摘要： GENE_NID=do.call(rbind, lapply(GENE_ID, as.integer)) 阅读全文

posted @ 2021-01-25 10:56 坐山雕阅读(71) 评论(0) 推荐(0)

R reorder data.frame column

摘要： PIN<- SSIN[, col_order_list] data_melt$ORDER<-factor(data_melt$variable,levels=COL_MERGE$Factor_Names) 阅读全文

posted @ 2021-01-23 11:52 坐山雕阅读(62) 评论(0) 推荐(0)

cluster BASIC

摘要： ####clusters. options (function() { var hsv2rgb = function(a,b,c) { var d=0,e=0,f=0,g=Math.floor(a*6),h=a*6-g,i=c*(1-b),j=c*(1-h*b),k=c*(1-(1-h)*b); s 阅读全文

posted @ 2021-01-22 17:04 坐山雕阅读(44) 评论(0) 推荐(0)

ssh,scp带密码操作

摘要： 1、远程执行，带密码参数 sshpass 安装命令： ```{sh} yum install sshpass ##执行命令： sshpass -p "mima" ssh root@localhost ## 参数小写p，密码mima ``` 2、非22端口 ssh -p 9062 111.111.11 阅读全文

posted @ 2021-01-22 16:16 坐山雕阅读(1351) 评论(0) 推荐(0)

R data.frame filter out rowsum==0 and colsum==0

摘要： SSIN0<-filter(SIN,rowSums(SIN)>0)SSIN<-SSIN0 %>% select(where(~ is.numeric(.x) && sum(.x) >10000 )) 阅读全文

posted @ 2021-01-22 15:00 坐山雕阅读(74) 评论(0) 推荐(0)

How to repeat loop n times in Bash

摘要： for (( i=0; i<10; ++i)); do [ -e filename ] && break sleep 10 done 阅读全文

posted @ 2021-01-20 16:43 坐山雕阅读(47) 评论(0) 推荐(0)

numpy.random.choice(a, size=None, replace=True, p=None)

摘要： #numpy.random.choice(a, size=None, replace=True, p=None) #从a(只要是ndarray都可以，但必须是一维的)中随机抽取数字，并组成指定大小(size)的数组 #replace:True表示可以取相同数字，False表示不可以取相同数字 #数组阅读全文

posted @ 2021-01-19 10:45 坐山雕阅读(73) 评论(0) 推荐(0)

transpose

摘要： import os,sysIN=sys.argv[1]#IN="matrix.CELL_TFYNSUM_HITSUM.plpc.sTNS.data.plpc.RPM"FIN=open(IN,"r")FOUT=open(IN+".t","w")D={}cn=0while True: line=FIN. 阅读全文

posted @ 2021-01-18 19:11 坐山雕阅读(47) 评论(0) 推荐(0)

\n ,

摘要： perl -pe 's/\n/$1,/' your_file 阅读全文

posted @ 2021-01-18 14:55 坐山雕阅读(159) 评论(0) 推荐(0)

R args

摘要： args = commandArgs(trailingOnly=TRUE) IN=args[1] 阅读全文

posted @ 2021-01-18 14:39 坐山雕阅读(88) 评论(0) 推荐(0)

导航

公告