Revision 469689991e7dbce2be4c4f618584304d91841c49 authored by Chase W. Nelson on 01 October 2020, 17:39 UTC, committed by Chase W. Nelson on 01 October 2020, 17:39 UTC
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images/cover_image2.png
images/cover_image_old.png
images/cover_image22.png
images/GITHUB PREVIEW.png
images/GITHUB PREVIEW_old.png
images/cover_image1.png
images/github_preview.png
data_zotero/Wuhan_Hu_1_genes.tsv
data_zotero/within-host_SNPGenie_byCodon.tsv
data_zotero/within-host_SNPGenie.tsv
data_zotero/within-host_OLGenie.tsv
data_zotero/within-host_FINAL.tsv
data_zotero/short_unannot_ORFs_aa.fasta
data_zotero/selection_three_levels.tsv
data_zotero/SARS-related-CoV_ALN.gtf
data_zotero/SARS-related-CoV_ALN.fasta
data_zotero/SARS-ref_ORF3a_ss13_windows.tsv
data_zotero/SARS-ref_N_ss13_windows.tsv
data_zotero/SARS-CoV-2.gtf
data_zotero/SARS-CoV-2-ref_ORF3a_ss12_windows_pangolin.tsv
data_zotero/SARS-CoV-2-ref_ORF3a_ss12_windows.tsv
data_zotero/SARS-CoV-2-ref_N_ss13_windows.tsv
data_zotero/riboseq_upstream_peaks.tsv
data_zotero/riboseq_sample_metadata.tsv
data_zotero/ranodmized_M_aa.fasta
data_zotero/randomized_S_aa.fasta
data_zotero/randomized_ORF9c_aa.fasta
data_zotero/randomized_ORF9b_aa.fasta
data_zotero/randomized_ORF8_aa.fasta
data_zotero/randomized_ORF7b_aa.fasta
data_zotero/randomized_ORF7a_aa.fasta
data_zotero/randomized_ORF6_aa.fasta
data_zotero/randomized_ORF3d_aa.fasta
data_zotero/randomized_ORF3d2_aa.fasta
data_zotero/randomized_ORF3c_aa.fasta
data_zotero/randomized_ORF3b_aa.fasta
data_zotero/randomized_ORF3a_aa.fasta
data_zotero/randomized_ORF10_aa.fasta
data_zotero/randomized_N_aa.fasta
data_zotero/randomized_E_aa.fasta
data_zotero/ORF_length_heatmap_data.tsv
data_zotero/NetMHCpan_Wuhan-Hu-1_additional.tsv
data_zotero/NetMHCpan_Wuhan-Hu-1.tsv
data_zotero/NetMHCpan_S_random_tally.tsv
data_zotero/NetMHCpan_ORF9c_random_tally.tsv
data_zotero/NetMHCpan_ORF9b_random_tally.tsv
data_zotero/NetMHCpan_ORF8_random_tally.tsv
data_zotero/NetMHCpan_ORF7b_random_tally.tsv
data_zotero/NetMHCpan_ORF7a_random_tally.tsv
data_zotero/NetMHCpan_ORF6_random_tally.tsv
data_zotero/NetMHCpan_ORF3d_random_tally.tsv
data_zotero/NetMHCpan_ORF3d2_random_tally.tsv
data_zotero/NetMHCpan_ORF3c_random_tally.tsv
data_zotero/NetMHCpan_ORF3b_random_tally.tsv
data_zotero/NetMHCpan_ORF3a_random_tally.tsv
data_zotero/NetMHCpan_ORF10_random_tally.tsv
data_zotero/NetMHCpan_N_random_tally.tsv
data_zotero/NetMHCpan_M_random_tally.tsv
data_zotero/NetMHCpan_E_random_tally.tsv
data_zotero/NetMHCIIpan_Wuhan-Hu-1_additional.txt
data_zotero/NetMHCIIpan_Wuhan-Hu-1.txt
data_zotero/NetMHCIIpan_S_random_tally.tsv
data_zotero/NetMHCIIpan_ORF9c_random_tally.tsv
data_zotero/NetMHCIIpan_ORF9b_random_tally.tsv
data_zotero/NetMHCIIpan_ORF8_random_tally.tsv
data_zotero/NetMHCIIpan_ORF7b_random_tally.tsv
data_zotero/NetMHCIIpan_ORF7a_random_tally.tsv
data_zotero/NetMHCIIpan_ORF6_random_tally.tsv
data_zotero/NetMHCIIpan_ORF3d_random_tally.tsv
data_zotero/NetMHCIIpan_ORF3d2_random_tally.tsv
data_zotero/NetMHCIIpan_ORF3c_random_tally.tsv
data_zotero/NetMHCIIpan_ORF3b_random_tally.tsv
data_zotero/NetMHCIIpan_ORF3a_random_tally.tsv
data_zotero/NetMHCIIpan_ORF10_random_tally.tsv
data_zotero/NetMHCIIpan_N_random_tally.tsv
data_zotero/NetMHCIIpan_M_random_tally.tsv
data_zotero/NetMHCIIpan_E_random_tally.tsv
data_zotero/MHCII_short_unannot_ORFs_tally.tsv
data_zotero/MHCII_short_unannot_ORFs_stripped.tsv
data_zotero/MHCII_short_unannot_ORFs.tsv
data_zotero/MHCII_epitope_summary_test.tsv
data_zotero/MHCII_epitope_summary_tally.tsv
data_zotero/MHCII_epitope_summary.tsv
data_zotero/MHCI_short_unannot_ORFs.tsv
data_zotero/MHCI_epitope_summary_test.tsv
data_zotero/MHCI_epitope_summary_tally.tsv
data_zotero/MHCI_epitope_summary.tsv
data_zotero/mass-spec_data.tsv
data_zotero/mapped_reads_by_readlength_wCDS.tsv
data_zotero/mapped_reads_by_readlength_sumSamples_win30read30.tsv
data_zotero/mapped_reads_by_readlength_sumSamples_win30read29.tsv
data_zotero/mapped_reads_by_readlength_sumSamples_win29read30.tsv
data_zotero/mapped_reads_by_readlength_sumSamples_win29read29.tsv
data_zotero/mapped_reads_by_readlength_sumSamples_win19read30.tsv
data_zotero/mapped_reads_by_readlength_sumSamples_win19read29.tsv
data_zotero/mapped_reads_by_readlength.tsv
data_zotero/hydrophobicity_profiles_ORF3a_corr.tsv
data_zotero/hydrophobicity_profiles_ORF3a.csv
data_zotero/gene_position_joiner.tsv
data_zotero/frameshift_results.txt
data_zotero/frames_table.txt
data_zotero/expression_data_by_gene_frame.tsv
data_zotero/expression_data_by_gene.tsv
data_zotero/between-taxa_SNPGenie_taxaRestricted.tsv
data_zotero/between-taxa_SNPGenie.tsv
data_zotero/between-taxa_OLGenie_addNN.tsv
data_zotero/between-taxa_OLGenie2.tsv
data_zotero/between-taxa_OLGenie.tsv
data_zotero/between-taxa_FINAL.tsv
data_zotero/between-taxa_codon_OL_category.tsv
data_zotero/between-host_SNPGenie.tsv
data_zotero/between-host_OLGenie.tsv
data_zotero/between-host_FINAL.tsv
.Rhistory
data_zotero/NC_045512_site_database_altA.tsv
data_zotero/NC_045512_site_database_altC.tsv
data_zotero/NC_045512_site_database_altG.tsv
data_zotero/NC_045512_site_database_altT.tsv
data_zotero/SARSCOV2_MAFFT_processed_variants_MAF0.02_ManualCheck_Fig7.xlsx
data/SARS-related-CoV_ALN.gtf.txt
data_zotero/between-host_FINAL.txt
data_zotero/between-host_OLGenie.txt
data_zotero/between-host_SNPGenie.txt
data_zotero/between-taxa_codon_OL_category.txt
data_zotero/between-taxa_FINAL.txt
data_zotero/between-taxa_OLGenie.txt
data_zotero/between-taxa_OLGenie2.txt
data_zotero/between-taxa_OLGenie_addNN.txt
data_zotero/between-taxa_SNPGenie.txt
data_zotero/between-taxa_SNPGenie_taxaRestricted.txt
data_zotero/expression_data_by_gene.txt
data_zotero/expression_data_by_gene_frame.txt
data_zotero/gene_position_joiner.txt
data_zotero/hydrophobicity_profiles_ORF3a_corr.txt
data_zotero/mapped_reads_by_readlength.txt
data_zotero/mapped_reads_by_readlength_sumSamples_win19read29.txt
data_zotero/mapped_reads_by_readlength_sumSamples_win19read30.txt
data_zotero/mapped_reads_by_readlength_sumSamples_win29read29.txt
data_zotero/mapped_reads_by_readlength_sumSamples_win29read30.txt
data_zotero/mapped_reads_by_readlength_sumSamples_win30read29.txt
data_zotero/mapped_reads_by_readlength_sumSamples_win30read30.txt
data_zotero/mapped_reads_by_readlength_wCDS.txt
data_zotero/mass-spec_data.txt
data_zotero/MHCI_epitope_summary.txt
data_zotero/MHCI_epitope_summary_tally.txt
data_zotero/MHCI_epitope_summary_test.txt
data_zotero/MHCI_short_unannot_ORFs.txt
data_zotero/MHCII_epitope_summary.txt
data_zotero/MHCII_epitope_summary_tally.txt
data_zotero/MHCII_epitope_summary_test.txt
data_zotero/MHCII_short_unannot_ORFs.txt
data_zotero/MHCII_short_unannot_ORFs_stripped.txt
data_zotero/MHCII_short_unannot_ORFs_tally.txt
data_zotero/NetMHCIIpan_E_random_tally.txt
data_zotero/NetMHCIIpan_M_random_tally.txt
data_zotero/NetMHCIIpan_N_random_tally.txt
data_zotero/NetMHCIIpan_ORF10_random_tally.txt
data_zotero/NetMHCIIpan_ORF3a_random_tally.txt
data_zotero/NetMHCIIpan_ORF3b_random_tally.txt
data_zotero/NetMHCIIpan_ORF3c_random_tally.txt
data_zotero/NetMHCIIpan_ORF3d2_random_tally.txt
data_zotero/NetMHCIIpan_ORF3d_random_tally.txt
data_zotero/NetMHCIIpan_ORF6_random_tally.txt
data_zotero/NetMHCIIpan_ORF7a_random_tally.txt
data_zotero/NetMHCIIpan_ORF7b_random_tally.txt
data_zotero/NetMHCIIpan_ORF8_random_tally.txt
data_zotero/NetMHCIIpan_ORF9b_random_tally.txt
data_zotero/NetMHCIIpan_ORF9c_random_tally.txt
data_zotero/NetMHCIIpan_S_random_tally.txt
data_zotero/NetMHCpan_E_random_tally.txt
data_zotero/NetMHCpan_M_random_tally.txt
data_zotero/NetMHCpan_N_random_tally.txt
data_zotero/NetMHCpan_ORF10_random_tally.txt
data_zotero/NetMHCpan_ORF3a_random_tally.txt
data_zotero/NetMHCpan_ORF3b_random_tally.txt
data_zotero/NetMHCpan_ORF3c_random_tally.txt
data_zotero/NetMHCpan_ORF3d2_random_tally.txt
data_zotero/NetMHCpan_ORF3d_random_tally.txt
data_zotero/NetMHCpan_ORF6_random_tally.txt
data_zotero/NetMHCpan_ORF7a_random_tally.txt
data_zotero/NetMHCpan_ORF7b_random_tally.txt
data_zotero/NetMHCpan_ORF8_random_tally.txt
data_zotero/NetMHCpan_ORF9b_random_tally.txt
data_zotero/NetMHCpan_ORF9c_random_tally.txt
data_zotero/NetMHCpan_S_random_tally.txt
data_zotero/NetMHCpan_Wuhan-Hu-1.txt
data_zotero/NetMHCpan_Wuhan-Hu-1_additional.txt
data_zotero/ORF_length_heatmap_data.txt
data_zotero/riboseq_sample_metadata.txt
data_zotero/riboseq_upstream_peaks.txt
data_zotero/SARS-CoV-2-ref_N_ss13_windows.txt
data_zotero/SARS-CoV-2-ref_ORF3a_ss12_windows_pangolin.txt
data_zotero/SARS-CoV-2-ref_ORF3a_ss12_windows_prepangolin.txt
data_zotero/SARS-CoV-ref_N_ss13_windows.txt
data_zotero/SARS-CoV-ref_ORF3a_ss13_windows.txt
data_zotero/selection_three_levels.txt
data_zotero/within-host_FINAL.txt
data_zotero/within-host_OLGenie.txt
data_zotero/within-host_SNPGenie.txt
data_zotero/within-host_SNPGenie_byCodon.txt
data_zotero/Wuhan_Hu_1_genes.txt
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