Files in ramadatta/CPgeneProfiler
Profiles the Carbapenamase genes from the genome assemblies (One Line, Title Case)
CPgeneProfiler.Rproj
Code_of_Conduct.md
DESCRIPTION
LICENSE.md
NAMESPACE
R/CPcontlen.R
R/CPgeneProfiler.R
R/assemblystat.R
R/cocarriage.R
R/cp_summarize.R
R/cpblast.R
R/cpcore.R
R/cpprofile.R
R/db_summary.R
R/files2move.R
R/filt_blast.R
R/jpeg2pdf.R
R/jpeg_merge.R
R/pdfs2pdf.R
R/plot_conlen.R
R/png2pdf.R
R/png_merge.R
R/tiff2pdf.R
R/tiff_merge.R
R/upsetR_plot.R
README.md
as1_2.png
cpprof_upset.png
image.jpg
len1_2.png
man/CPcontlen.Rd
man/CPgeneProfiler.Rd
man/assemblystat.Rd
man/cocarriage.Rd
man/cp_summarize.Rd
man/cpblast.Rd
man/cpcore.Rd
man/cpprofile.Rd
man/db_summary.Rd
man/files2move.Rd
man/filt_blast.Rd
man/jpeg2pdf.Rd
man/jpeg_merge.Rd
man/pdfs2pdf.Rd
man/plot_conlen.Rd
man/png2pdf.Rd
man/png_merge.Rd
man/tiff2pdf.Rd
man/tiff_merge.Rd
man/upsetR_plot.Rd
paper.bib
paper.md
testData/db/NCBI_BARRGD_CPG_DB.fasta
testData/fasta/genome_001.fasta
testData/fasta/genome_002.fasta
testData/fasta/genome_003.fasta
testData/fasta/genome_004.fasta
testData/fasta/genome_005.fasta
testData/fasta/genome_006.fasta
testData/fasta/genome_007.fasta
testData/fasta/genome_008.fasta
testData/fasta/genome_009.fasta
testData/fasta/genome_010.fasta
testData/fasta/genome_011.fasta
testData/fasta/genome_012.fasta
testData/fasta/genome_013.fasta
testData/fasta/genome_014.fasta
testData/fasta/genome_015.fasta
testData_Output/1_CP_BLAST_Results/blastResults.filt.txt
testData_Output/1_CP_BLAST_Results/blastResults.txt
testData_Output/2_Cocarriage_Results/Co-carriage_Report.txt
testData_Output/2_Cocarriage_Results/Cocarriage_combinedResults.txt
testData_Output/2_Cocarriage_Results/DiffCP_DiffContig.txt
testData_Output/2_Cocarriage_Results/DiffCP_SameContig.txt
testData_Output/2_Cocarriage_Results/SameCP_DiffContig.txt
testData_Output/2_Cocarriage_Results/SameCP_SameContig.txt
testData_Output/3_CP_Gene_Profile/CPgeneProfile.pdf
testData_Output/3_CP_Gene_Profile/CPgeneProfile.png
testData_Output/3_CP_Gene_Profile/cp_presence-absence_matrix.csv
testData_Output/4_CPGeneContig_LengthDistribution/CPContigSizeDist.txt
testData_Output/4_CPGeneContig_LengthDistribution/Contig_Distribution.pdf
testData_Output/4_CPGeneContig_LengthDistribution/KPC-2_Contig_Dist.png
testData_Output/4_CPGeneContig_LengthDistribution/NDM-1_Contig_Dist.png
testData_Output/4_CPGeneContig_LengthDistribution/OXA-181_Contig_Dist.png
testData_Output/5_Assembly_Stats/N50.png
testData_Output/5_Assembly_Stats/N50_N90.pdf
testData_Output/5_Assembly_Stats/N90.png
testData_Output/5_Assembly_Stats/assemblyStats.txt
testData_Output/6_UpsetR_Intersection_Plot/upset_plot.pdf
testData_Output/6_UpsetR_Intersection_Plot/upset_plot.png
testData_Output/SummaryPlots.pdf
