Files in abseqR
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

NEWS

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

R/abundanceAnalysis.R R/statistics.R R/diversityAnalysis.R R/util.R R/upstreamAnalysis.R R/pairwise.R R/AbSeqRep.R R/distributions.R R/plotter.R R/AbSeqCRep.R R/primerAnalysis.R R/annotationAnalysis.R R/productivityAnalysis.R R/accessors-AbSeq.R R/abseqReport.R vignettes/abseqR.Rmd

vignettes/abseq_workflow_MA.jpg

vignettes/simulation_flowchart_full.jpg

vignettes/post_report_fs.png

man/figures/README

tests/testthat.R tests/testthat/test_abseqReport.R tests/testthat/test_AbSeqRep.R tests/testthat/test_AbSeqCRep.R tests/testthat/test_report.R inst/doc/abseqR.R inst/doc/abseqR.Rmd inst/doc/abseqR.pdf inst/extdata/index.Rmd inst/extdata/template.Rmd

inst/extdata/ex/auxiliary/PCR2/analysis.params

inst/extdata/ex/auxiliary/PCR2/summary.txt

inst/extdata/ex/auxiliary/PCR2/annot/analysis.params

inst/extdata/ex/auxiliary/PCR2/annot/PCR2_all_clones_len_dist_no_outliers.csv

inst/extdata/ex/auxiliary/PCR2/annot/PCR2_all_clones_len_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/analysis.params

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_productivity.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igj_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_stopcodon_region_inframe.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_vjframe_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_stopcodon_dist_in_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_productive.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_stopcodon_region_outframe.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igd_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_inframe_unproductive.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igj_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igd_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR2/abundance/analysis.params

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_start_hm.tsv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_bitscore_hm.tsv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_mismatches_hm.tsv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_gene_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igj_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igj_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_gene_level.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_gaps_hm.tsv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_vjassoc.csv

inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_identity_hm.tsv

inst/extdata/ex/auxiliary/PCR2/diversity/analysis.params

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_duplication.csv

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/diversity_indices.tsv

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/lower_bound_estimate.tsv

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_duplication.csv

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_duplication.csv

inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR3/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR3/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/CDR1/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/CDR1/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/CDR3/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/CDR3/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR2/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR2/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/CDR2/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/CDR2/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR1/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR1/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR4/PCR2_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR4/PCR2_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr3_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr3_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr2_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr4_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr3_spectratype_no_outliers.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_v_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr2_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr1_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr1_spectratype.csv

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_v_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr3_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr1_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr3_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_v_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr1_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr4_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr2_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr2_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr3_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr4_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr1_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr1_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr2_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_fr2_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr3_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/analysis.params

inst/extdata/ex/auxiliary/PCR3/summary.txt

inst/extdata/ex/auxiliary/PCR3/annot/PCR3_all_clones_len_dist.csv

inst/extdata/ex/auxiliary/PCR3/annot/analysis.params

inst/extdata/ex/auxiliary/PCR3/annot/PCR3_all_clones_len_dist_no_outliers.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/analysis.params

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_inframe_unproductive.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_productivity.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igj_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igd_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_productive.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igd_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_region_outframe.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igj_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_vjframe_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_region_inframe.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr2_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr2_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr2_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_dist_in_frame.csv

inst/extdata/ex/auxiliary/PCR3/abundance/analysis.params

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_gene_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_vjassoc.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igj_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igj_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_gaps_hm.tsv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_gene_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_mismatches_hm.tsv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_bitscore_hm.tsv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_start_hm.tsv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_identity_hm.tsv

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_duplication.csv

inst/extdata/ex/auxiliary/PCR3/diversity/analysis.params

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/diversity_indices.tsv

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/lower_bound_estimate.tsv

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_duplication.csv

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_duplication.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR3/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR3/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/CDR1/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/CDR1/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/CDR3/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/CDR3/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR2/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR2/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/CDR2/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/CDR2/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR1/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR1/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR4/PCR3_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR3/diversity/composition_logos/FR4/PCR3_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr1_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr3_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr4_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_v_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr3_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr2_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr2_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr1_spectratype.csv

inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr3_spectratype_no_outliers.csv

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr2_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr2_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr3_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr1_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr3_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_v_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr4_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_v_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr1_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr3_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr4_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr2_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr3_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr1_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr1_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr2_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/analysis.params

inst/extdata/ex/auxiliary/PCR1/summary.txt

inst/extdata/ex/auxiliary/PCR1/annot/analysis.params

inst/extdata/ex/auxiliary/PCR1/annot/PCR1_all_clones_len_dist.csv

inst/extdata/ex/auxiliary/PCR1/annot/PCR1_all_clones_len_dist_no_outliers.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_dist_in_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/analysis.params

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igj_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igj_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igd_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_region_inframe.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_productivity.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_productive.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_gaps_dist_out_of_frame.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igd_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_inframe_unproductive.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_region_outframe.csv

inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_vjframe_dist.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_gaps_hm.tsv

inst/extdata/ex/auxiliary/PCR1/abundance/analysis.params

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igj_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igd_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_variant_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_gene_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igd_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_start_hm.tsv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_vjassoc.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_identity_hm.tsv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igd_dist_gene_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_mismatches_dist.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igj_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_gaps_dist.csv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_bitscore_hm.tsv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_mismatches_hm.tsv

inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_family_level.csv

inst/extdata/ex/auxiliary/PCR1/diversity/analysis.params

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_v_duplication.csv

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_duplication.csv

inst/extdata/ex/auxiliary/PCR1/diversity/diversity_indices.tsv

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_fr_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_fr_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_v_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_rarefaction.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/lower_bound_estimate.tsv

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_v_recapture.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_fr_duplication.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR3/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR3/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/CDR1/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/CDR1/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/CDR3/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/CDR3/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR2/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR2/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/CDR2/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/CDR2/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR1/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR1/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR4/PCR1_cumulative_logo_raw.csv

inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR4/PCR1_cumulative_logo.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr2_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr3_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr1_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr3_spectratype_no_outliers.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_v_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr3_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr2_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr4_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr1_spectratype.csv

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr1_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr4_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr2_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr3_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr1_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr1_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_v_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr3_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr2_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr2_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr3_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr3_clonotypes_all_over.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_v_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr4_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr2_clonotypes_all_under.csv.gz

inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr1_clonotypes_all_under.csv.gz

inst/extdata/ex/hdf/README

inst/script/ex.md

inst/script/index.txt

inst/script/template.txt

abseqR documentation built on Nov. 8, 2020, 8:28 p.m.

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abseqR Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

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abseqR
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

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Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries