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1. ShinyExtras ShinyExtras Public

   R

2. genescf/GeneSCF genescf/GeneSCF Public

   Gene Set Clustering based on Functional annotation

   Perl 22 5

3. TransExtract_betaV1.2 TransExtract_betaV1.2 Public

   Extract Transitions from PARCLIP data. This is beta version, this can be improved by including more description about the results and also with graphical visualization.

   Perl 1

4. RNA-seq read count normalization (TP... RNA-seq read count normalization (TPM and RPKM)

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   #Rscript normalize_featurecounts.R counts_table.txt tpm ;

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   #Rscript normalize_featurecounts.R counts_table.txt rpkm ;

   3

   4

   #Sample table###

   5

5. rpkm_rnaseq_count rpkm_rnaseq_count Public

   RPKM for RNASeq counts

   Perl 16 12

6. Check the Phred Scale quality of seq... Check the Phred Scale quality of sequencing files

   1

   #!/bin/bash

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   # ./CheckPhredScale.sh <FASTQ_FILE> <NUMBER OF LINES TO CHECK>

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   echo "Shell:";

   4

   5

   zcat $1 | head -n $2 | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding";}';