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  1. ShinyExtras ShinyExtras Public

    R

  2. genescf/GeneSCF genescf/GeneSCF Public

    Gene Set Clustering based on Functional annotation

    Perl 21 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)
    1
    #Rscript normalize_featurecounts.R counts_table.txt tpm ;
    2
    #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
    2
    # ./CheckPhredScale.sh <FASTQ_FILE> <NUMBER OF LINES TO CHECK>
    3
    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";}';