My PERL and other UNIX based codes developed while analysing NGS, microarray other data.
#CONTENTS
├── NGS
│ ├── Bash
│ │ └── SAM_to_BAM.sh
│ └── PERL
│ ├── bamCoverageCalc.pl
│ ├── Batch_tview.pl
│ └── generate_QC_plots_R_script.pl
├── Phylogenetics
│ └── Color_node_figtree.pl
├── R
│ ├── Basic_microarray-analysis.R
│ └── oligo-limma-pipeline.docx
├── README.md
├── samtools_mpileup
│ └── vcf
│ └── multiSample_process.pl
└── Utilities
├── compareTables.pl
├── Download_ncbi_SRA.pl
├── extract_snp_flank.pl
├── GO_enrichment.pl
├── HMMScanParser.pl
├── OneLiners.txt
├── shanon_entropy_from_MSA.pl
└── subSet_PfamA.pl
I will be glad hearing back from you. Please write your feedback/feature request to me. If you have a Git-hub account use the 'Issue' link at the top of this page. You may write directly to me via email (kcm.eid[at]gmail.com).
PS: Using :r !date insert time stamp in Vim.
Wed Oct 28 15:34:40 IST 2015
- first script added; samtools_mpileup/vcf
Thu Dec 3 13:03:46 IST 2015 2. Few NGS scripts added
- Thu Dec 10 12:48:30 AM IST 2015: Utilities: GO enrichment script;
- Mon Jan 1 11:34:45 PM IST 2016: Utilities: extract_snp_flank.pl
- Qua Abr 13 16:34:54 BRT 2016: Utilities: pfamparser.pl
- Qua Abr 13 17:33:23 BRT 2016 : NGS: PERL: New scipts Fastq_boxplot and batch_Tview.pl added; shanon_antropy_calc.pl
- Wed June 22 11:01 BRT 2016 : Utilites: new scripts added: compareTables.pl, Download_ncbi_SRA.pl , subSet_PfamA.pl, R folder added
- Sun Oct 22 2017: Python section added