置顶 · 薛良交-南京林业大学林学院

2019-11-6 20:06

http://linxue.njfu.edu.cn/sz/ShowJs.asp?id=358 http://linxue.njfu.edu.cn/info.php?cid=117 姓名： 薛良交 系别： 林木遗传育种系 职务： 教师 类别： 教授 最终学历： 博士研究生 最终学位： 理学博士 办公电话： 电子邮箱： lxue@njfu.edu.cn 教育经历： ...

个人分类: Bioinformatics|6944 次阅读|没有评论

R语言加速

薛良交 2015-5-5 21:26

发现不少人写了介绍： 英文版： http://www.r-bloggers.com/faster-higher-stonger-a-guide-to-speeding-up-r-code-for-busy-people/ 中文版： http://www.seekingqed.com/programming/r/accelerate_r 总结一下： 运行速度，Rcpp Parallel Processing compiler 编程所花时间，也是这个顺序。 ...

个人分类: Bioinformatics|3768 次阅读|没有评论

JC10: SNPlice, SNP and alternative splicing

薛良交 2015-4-17 01:58

Bioinformatics. 2015 Apr 15;31(8):1191-8. doi: 10.1093/bioinformatics/btu804. Epub 2014 Dec 6. SNPlice: variants that modulate Intron retention from RNA-sequencing data. Mudvari P1, Movassagh M1, Kowsari K1, Seyfi A1, Kokkinaki M2, Edwards NJ2, Golestaneh N3, Horvath A1. Author information Abst ...

个人分类: Bioinformatics|2417 次阅读|没有评论

Independent filtering & high-throughput experiments

薛良交 2015-4-5 07:49

http://www.pnas.org/content/107/21/9546.long Independent filtering increases detection power for high-throughput experiments We all may know this during the practice of data analysis. They got it published, on PNAS.

个人分类: Bioinformatics|2434 次阅读|没有评论

文本文件分行

薛良交 2015-3-5 11:01

众口难调。 简单个分行符，各个操作系统都个不相同。Windows: rn, Unix: n Old version of Mac: r. 写个程序要让各个系统都适用，也挺折腾。 ## 小文件可以这样，都读进来，再拆分 local $/ = undef; my $content = DESIGN; my @lines = split /\r\n|\n|\r/, $content; ## 大文 ...

个人分类: Bioinformatics|2150 次阅读|没有评论

Two Packages for network analysis: Bipartite and qgraph

薛良交 2015-2-19 23:00

http://sachaepskamp.com/qgraph https://solomonmessing.wordpress.com/2012/09/30/working-with-bipartiteaffiliation-network-data-in-r/ http://www.inside-r.org/packages/cran/bipartite/docs/czvalues

个人分类: Bioinformatics|3512 次阅读|没有评论

Linux rename file names by batch

薛良交 2015-1-20 12:31

rename _namecounts.txt .txt *.txt for f in *.txt; do mv $f ${f/${f:4:8}/1}; done This is the correct version:   sed function sed s/^@RG.*/@RGtID:717tSM:sample1tPL:illuminatLB:lib1tPU:unit1/g 717RsRII_WGA_old.sam & ...

个人分类: Bioinformatics|2003 次阅读|没有评论

Parsing of CIGAR and MD tag in SAM/BAM format

薛良交 2015-1-1 01:05

Source code cigar http://cpansearch.perl.org/src/MNSMAR/GenOO-1.4.5/lib/GenOO/Data/File/SAM/Cigar.pm MDZ http://cpansearch.perl.org/src/MNSMAR/GenOO-1.4.5/lib/GenOO/Data/File/SAM/MDZ.pm Cigar and MDZ http://cpansearch.perl.org/src/MNSMAR/GenOO-1.4.5/lib/GenOO/Data/File ...

个人分类: Bioinformatics|5400 次阅读|没有评论

向NCBI SRA提交数据

薛良交 2014-11-15 05:17

0 Collect description information, prepare read files. Run md5sum (Linux) to get the md5 numbers of read files 1 Create BioProject Go to: http://www.ncbi.nlm.nih.gov/books/NBK47529/ Steps for SRA Submission-- Create a B ...

个人分类: Bioinformatics|10036 次阅读|没有评论

PSL format for blat software

薛良交 2014-11-10 02:56

https://www.biostars.org/p/44633/ In general the coordinates in psl files are “zero based half open.” The first base in a sequence is numbered zero rather than one. When representing a range the end coordinate is not included in the range. Thus the first 100 bases of a sequence are represente ...

个人分类: Bioinformatics|3743 次阅读|没有评论

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