Files in nikopech/lineagespot
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
.Rbuildignore
.gitignore
CITATION.cff
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/get_lineage_report.R
R/lineagespot.R
R/lineagespot_hits.R
R/merge_vcf.R
R/uniq_variants.R
README.md
inst/extdata/NC_045512.2_annot.gff3
inst/extdata/ref/AY.1.txt
inst/extdata/ref/AY.2.txt
inst/extdata/ref/AY.3.1.txt
inst/extdata/ref/AY.3.txt
inst/extdata/ref/B.1.1.7+S_E484K.txt
inst/extdata/ref/B.1.1.7.txt
inst/extdata/ref/B.1.351.2.txt
inst/extdata/ref/B.1.351.3.txt
inst/extdata/ref/B.1.351.txt
inst/extdata/ref/B.1.617.2.txt
inst/extdata/ref/P.1.1.txt
inst/extdata/ref/P.1.2.txt
inst/extdata/ref/P.1.txt
inst/extdata/srep-article-code/Figure1/freebayes-vs-gatk.csv
inst/extdata/srep-article-code/Figure1/freebayes-vs-mpileup.csv
inst/extdata/srep-article-code/Figure1/gatk-vs-mpileup.csv
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_01_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_10_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_20_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_30_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_40_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_50_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_A_freebayes_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_01_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_10_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_20_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_30_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_40_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_50_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/Replicate_B_freebayes_ann.vcf
inst/extdata/srep-article-code/Figure1/input_files/SampleList
inst/extdata/srep-article-code/Figure1/input_files/meta-data.xlsx
inst/extdata/srep-article-code/Figure1/input_files/stats.txt
inst/extdata/srep-article-code/Figure1/plot_figure1.R
inst/extdata/srep-article-code/Figure2/Amino_acid_Abbreviations.txt
inst/extdata/srep-article-code/Figure2/gene-metadata.xlsx
inst/extdata/srep-article-code/Figure2/meta-data.xlsx
inst/extdata/srep-article-code/Figure2/plot_figure2.R
inst/extdata/srep-article-code/Figure2/sewage_VCFList.csv
inst/extdata/srep-article-code/Figure3/Amino_acid_Abbreviations.txt
inst/extdata/srep-article-code/Figure3/coverage-all-sewage-samples.csv
inst/extdata/srep-article-code/Figure3/meta-data.xlsx
inst/extdata/srep-article-code/Figure3/outbreakinfo_mutation_report_data_b.1.1.7.tsv
inst/extdata/srep-article-code/Figure3/outbreakinfo_mutation_report_data_b.1.351.tsv
inst/extdata/srep-article-code/Figure3/plot_figure3A.R
inst/extdata/srep-article-code/Figure3/plot_figure3B.R
inst/extdata/srep-article-code/Figure3/sewage_VCFList.csv
inst/extdata/srep-article-code/Figure4/Amino_acid_Abbreviations.txt
inst/extdata/srep-article-code/Figure4/Corrected_tables_v2.xlsx
inst/extdata/srep-article-code/Figure4/meta-data.xlsx
inst/extdata/srep-article-code/Figure4/outbreakinfo_mutation_report_data_B.1.1.7.tsv
inst/extdata/srep-article-code/Figure4/plot_figure4A.R
inst/extdata/srep-article-code/Figure4/plot_figure4BC.R
inst/extdata/srep-article-code/Figure4/results_B.1.1.7.csv
inst/extdata/srep-article-code/Figure4/unique_mutations_B.1.1.7.csv
inst/extdata/srep-article-code/README.md
inst/extdata/srep-article-code/create_map.R
inst/extdata/srep-article-code/figures.pptx
inst/extdata/vcf-files/SampleA_freebayes_ann.vcf
inst/extdata/vcf-files/SampleB_freebayes_ann.vcf
inst/extdata/vcf-files/SampleC_freebayes_ann.vcf
inst/scripts/README.md
inst/scripts/raw-data-analysis.md
man/get_lineage_report.Rd
man/lineagespot.Rd
man/lineagespot_hits.Rd
man/merge_vcf.Rd
man/uniq_variants.Rd
test.txt
vignettes/lineagespot.Rmd
