├── .gitignore ├── Implementation.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── RiboMiner ├── CoverageOfEachTrans.py ├── EnrichmentAnalysis.py ├── EnrichmentAnalysisForSingleTrans.py ├── ExtractSequenceCenteredOnAPosition.py ├── FunctionDefinition.py ├── GCContent.py ├── GetProteinCodingSequence.py ├── GetUTRSequences.py ├── LengthDistribution.py ├── MergeSampleDensitys.py ├── MetageneAnalysis.py ├── MetageneAnalysisForTheWholeRegions.py ├── ModifyHTseq.py ├── OutputTranscriptInfo.py ├── PausingScore.py ├── Periodicity.py ├── PlotEnrichmentRatio.py ├── PlotGCContent.py ├── PlotHydropathyCharge.py ├── PlotMetageneAnalysis.py ├── PlotMetageneAnalysisForTheWholeRegions.py ├── PlotPolarity.py ├── PlotRiboDensityAroundTriAAMotifs.py ├── PlotRiboDensityAtEachKindAAOrCodon.py ├── PlotTransCoverage.py ├── PolarityCalculation.py ├── ProcessPausingScore.py ├── RPFdist.py ├── ReadsLengthOfSpecificRegions.py ├── RiboDensityAroundTripleteAAMotifs.py ├── RiboDensityAtEachKindAAOrCodon.py ├── RiboDensityAtEachPosition.py ├── RiboDensityForSpecificRegion.py ├── RiboDensityOfDiffFrames.py ├── StatisticReadsOnDNAsContam.py ├── __init__.py ├── cAI.py ├── cAIPlot.py ├── enrichmentMeanDensity.py ├── hydropathyCharge.py ├── tAI.py └── tAIPlot.py ├── RuningTimeTest ├── Fly │ ├── code │ │ ├── DivideGeneSets.R │ │ ├── EA.sh │ │ ├── FA.sh │ │ ├── GetCdsSeqForGeneSets.sh │ │ ├── GetCommonGeneSets.R │ │ ├── MA.sh │ │ ├── QC.sh │ │ ├── fileTransfer.sh │ │ ├── prepare_references.sh │ │ └── seq2logo-2.1 │ │ │ ├── Seq2Logo.py │ │ │ ├── etc │ │ │ ├── B62_Reference_Distribution.pssm │ │ │ ├── Blosum62.txt │ │ │ ├── Seq2Logo_module.py │ │ │ └── logo_template.eps │ │ │ ├── release_notes.txt │ │ │ ├── seq2logo-2.1.all.tar.gz │ │ │ ├── seq2logo-2.1.readme │ │ │ └── test_data │ │ │ ├── blastprofile.txt │ │ │ ├── clustal.txt │ │ │ ├── fasta.txt │ │ │ ├── raw.txt │ │ │ └── weight.txt │ ├── data │ │ ├── 00.STAR │ │ │ └── README.txt │ │ ├── AA_charge.txt │ │ ├── Ref │ │ │ └── README.txt │ │ ├── attributes.txt │ │ ├── hydropathy.txt │ │ └── tRNA_GCNs_fly.txt │ └── results │ │ └── output │ │ ├── test_CDS_normed_mean_start codon.pdf │ │ ├── test_CDS_normed_mean_stop codon.pdf │ │ ├── test_Low-detergent-2_reading_frames.pdf │ │ ├── test_SRR3297803_DNA.pdf │ │ ├── test_SRR3297803_Intron.pdf │ │ ├── test_SRR3297803_RNA.pdf │ │ ├── test_SRR3297803_reads_distribution.txt │ │ ├── test_SRR3297803_reads_length.pdf │ │ ├── test_SRR3297803_start_periodicity.pdf │ │ ├── test_SRR3297803_stop_periodicity.pdf │ │ ├── test_UTR_normed_mean_start codon.pdf │ │ ├── test_UTR_normed_mean_stop codon.pdf │ │ ├── test_cAI_average_start codon.pdf │ │ ├── test_cAI_average_stop codon.pdf │ │ ├── test_mean_polarity.pdf │ │ ├── test_tAI_average_start codon.pdf │ │ ├── test_tAI_average_stop codon.pdf │ │ ├── test_whole_mean_metaplot.pdf │ │ ├── up_DDD_mean_density_on_triAAMotifs.pdf │ │ ├── up_KKK_mean_density_on_triAAMotifs.pdf │ │ ├── up_PPP_mean_density_on_triAAMotifs.pdf │ │ ├── up_density_on_each_kind_of_AA.pdf │ │ └── up_density_on_each_kind_of_codon.pdf ├── Human │ ├── AADensty.png │ ├── MA.png │ ├── QC.png │ ├── code │ │ ├── DivideGeneSets.R │ │ ├── EA.sh │ │ ├── FA.sh │ │ ├── GetCdsSeqForGeneSets.sh │ │ ├── GetCommonGeneSets.R │ │ ├── MA.sh │ │ ├── QC.sh │ │ ├── fileTransfer.sh │ │ ├── prepare_references.sh │ │ └── seq2logo-2.1 │ │ │ ├── Seq2Logo.py │ │ │ ├── etc │ │ │ ├── B62_Reference_Distribution.pssm │ │ │ ├── Blosum62.txt │ │ │ ├── Seq2Logo_module.py │ │ │ └── logo_template.eps │ │ │ ├── release_notes.txt │ │ │ ├── seq2logo-2.1.all.tar.gz │ │ │ ├── seq2logo-2.1.readme │ │ │ └── test_data │ │ │ ├── blastprofile.txt │ │ │ ├── clustal.txt │ │ │ ├── fasta.txt │ │ │ ├── raw.txt │ │ │ └── weight.txt │ ├── data │ │ ├── 00.STAR │ │ │ └── README.txt │ │ ├── AA_charge.txt │ │ ├── Ref │ │ │ └── README.txt │ │ ├── attributes_A.txt │ │ ├── attributes_P.txt │ │ ├── hydropathy.txt │ │ └── tRNA_GCNs_human.txt │ └── output │ │ ├── all_density_on_each_kind_of_AA.pdf │ │ ├── all_density_on_each_kind_of_codon.pdf │ │ ├── test_CDS_normed_mean_start codon.pdf │ │ ├── test_CDS_normed_mean_stop codon.pdf │ │ ├── test_Ctrl-1_reading_frames.pdf │ │ ├── test_SRR2873530_DNA.pdf │ │ ├── test_SRR2873530_Intron.pdf │ │ ├── test_SRR2873530_RNA.pdf │ │ ├── test_SRR2873530_reads_distribution.txt │ │ ├── test_SRR2873530_reads_length.pdf │ │ ├── test_SRR2873530_start_periodicity.pdf │ │ ├── test_SRR2873530_stop_periodicity.pdf │ │ ├── test_UTR_normed_mean_start codon.pdf │ │ ├── test_UTR_normed_mean_stop codon.pdf │ │ ├── test_cAI_average_start codon.pdf │ │ ├── test_cAI_average_stop codon.pdf │ │ ├── test_mean_polarity.pdf │ │ ├── test_mean_polarity_dataframe.txt │ │ ├── test_mean_polarity_dataframe.xlsx │ │ ├── test_tAI_average_start codon.pdf │ │ ├── test_tAI_average_stop codon.pdf │ │ ├── test_whole_mean_metaplot.pdf │ │ ├── up_DDD_mean_density_on_triAAMotifs.pdf │ │ ├── up_KKK_mean_density_on_triAAMotifs.pdf │ │ ├── up_PPP_mean_density_on_triAAMotifs.pdf │ │ ├── up_density_on_each_kind_of_AA.pdf │ │ └── up_density_on_each_kind_of_codon.pdf ├── Mouse │ ├── code │ │ ├── DivideGeneSets.R │ │ ├── EA.sh │ │ ├── FA.sh │ │ ├── GetCdsSeqForGeneSets.sh │ │ ├── GetCommonGeneSets.R │ │ ├── MA.sh │ │ ├── QC.sh │ │ ├── fileTransfer.sh │ │ ├── prepare_references.sh │ │ └── seq2logo-2.1 │ │ │ ├── Seq2Logo.py │ │ │ ├── etc │ │ │ ├── B62_Reference_Distribution.pssm │ │ │ ├── Blosum62.txt │ │ │ ├── Seq2Logo_module.py │ │ │ └── logo_template.eps │ │ │ ├── release_notes.txt │ │ │ ├── seq2logo-2.1.all.tar.gz │ │ │ ├── seq2logo-2.1.readme │ │ │ └── test_data │ │ │ ├── blastprofile.txt │ │ │ ├── clustal.txt │ │ │ ├── fasta.txt │ │ │ ├── raw.txt │ │ │ └── weight.txt │ ├── data │ │ ├── 00.STAR │ │ │ └── README.txt │ │ ├── AA_charge.txt │ │ ├── Ref │ │ │ └── README.txt │ │ ├── attributes.txt │ │ ├── hydropathy.txt │ │ └── tRNA_GCNs_mouse.txt │ └── results │ │ └── output │ │ ├── test_CDS_normed_mean_start codon.pdf │ │ ├── test_CDS_normed_mean_stop codon.pdf │ │ ├── test_Ctrl-2_reading_frames.pdf │ │ ├── test_SRR649755_DNA.pdf │ │ ├── test_SRR649755_Intron.pdf │ │ ├── test_SRR649755_RNA.pdf │ │ ├── test_SRR649755_reads_distribution.txt │ │ ├── test_SRR649755_reads_length.pdf │ │ ├── test_SRR649755_start_periodicity.pdf │ │ ├── test_SRR649755_stop_periodicity.pdf │ │ ├── test_UTR_normed_mean_start codon.pdf │ │ ├── test_UTR_normed_mean_stop codon.pdf │ │ ├── test_cAI_average_start codon.pdf │ │ ├── test_cAI_average_stop codon.pdf │ │ ├── test_charge_average_start codon.pdf │ │ ├── test_charge_average_stop codon.pdf │ │ ├── test_hydro_average_start codon.pdf │ │ ├── test_hydro_average_stop codon.pdf │ │ ├── test_mean_polarity.pdf │ │ ├── test_tAI_average_start codon.pdf │ │ ├── test_tAI_average_stop codon.pdf │ │ ├── test_whole_mean_metaplot.pdf │ │ ├── up.pdf │ │ ├── up_DDD_mean_density_on_triAAMotifs.pdf │ │ ├── up_KKK_mean_density_on_triAAMotifs.pdf │ │ ├── up_PPP_mean_density_on_triAAMotifs.pdf │ │ ├── up_density_on_each_kind_of_AA.pdf │ │ └── up_density_on_each_kind_of_codon.pdf └── Yeast │ ├── code │ ├── DivideGeneSets.R │ ├── EA.sh │ ├── FA.sh │ ├── GetCdsSeqForGeneSets.sh │ ├── GetCommonGeneSets.R │ ├── MA.sh │ ├── QC.sh │ ├── fileTransfer.sh │ ├── prepare_references.sh │ └── seq2logo-2.1 │ │ ├── Seq2Logo.py │ │ ├── etc │ │ ├── B62_Reference_Distribution.pssm │ │ ├── Blosum62.txt │ │ ├── Seq2Logo_module.py │ │ └── logo_template.eps │ │ ├── release_notes.txt │ │ ├── seq2logo-2.1.all.tar.gz │ │ ├── seq2logo-2.1.readme │ │ └── test_data │ │ ├── blastprofile.txt │ │ ├── clustal.txt │ │ ├── fasta.txt │ │ ├── raw.txt │ │ └── weight.txt │ ├── data │ ├── 00.STAR │ │ └── README.txt │ ├── AA_charge.txt │ ├── Ref │ │ └── README.txt │ ├── attributes.txt │ ├── hydropathy.txt │ ├── noncontam_SRR5008135.fastq │ └── tRNA_GCNs_Saccharomyces_cerevisiae.txt │ └── results │ └── output │ ├── eIF5A_CDS_normed_mean_start codon.pdf │ ├── eIF5A_CDS_normed_mean_stop codon.pdf │ ├── eIF5A_SRR5008135_DNA.pdf │ ├── eIF5A_SRR5008135_Intron.pdf │ ├── eIF5A_SRR5008135_RNA.pdf │ ├── eIF5A_SRR5008135_reads_distribution.txt │ ├── eIF5A_SRR5008135_reads_length.pdf │ ├── eIF5A_SRR5008135_start_periodicity.pdf │ ├── eIF5A_SRR5008135_stop_periodicity.pdf │ ├── eIF5A_UTR_normed_mean_start codon.pdf │ ├── eIF5A_UTR_normed_mean_stop codon.pdf │ ├── eIF5A_cAI_average_start codon.pdf │ ├── eIF5A_cAI_average_stop codon.pdf │ ├── eIF5A_mean_polarity.pdf │ ├── eIF5A_si-Ctrl-2_reading_frames.pdf │ ├── eIF5A_tAI_average_start codon.pdf │ ├── eIF5A_tAI_average_stop codon.pdf │ ├── eIF5A_whole_mean_metaplot.pdf │ ├── up.pdf │ ├── up_DDD_mean_density_on_triAAMotifs.pdf │ ├── up_KKK_mean_density_on_triAAMotifs.pdf │ ├── up_PPP_mean_density_on_triAAMotifs.pdf │ ├── up_density_on_each_kind_of_AA.pdf │ └── up_density_on_each_kind_of_codon.pdf ├── data ├── AA_charge_index.txt ├── hg38.longest.transcripts.info.txt ├── hg38.transInfo.txt ├── hydropathy_index.txt ├── tRNA_GCNs_Saccharomyces cerevisiae.txt ├── tRNA_GCNs_fly.txt ├── tRNA_GCNs_human.txt └── 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