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

NEWS
LICENSE
DESCRIPTION
README.md
NAMESPACE
inst/doc/abseqR.R inst/doc/abseqR.pdf inst/doc/abseqR.Rmd
inst/script/template.txt
inst/script/ex.md
inst/script/index.txt
inst/extdata/template.Rmd inst/extdata/index.Rmd
inst/extdata/ex/auxiliary/PCR1/analysis.params
inst/extdata/ex/auxiliary/PCR1/summary.txt
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_duplication.csv
inst/extdata/ex/auxiliary/PCR1/diversity/analysis.params
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_fr_duplication.csv
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_v_duplication.csv
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_rarefaction.csv.gz
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_cdr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr1_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_v_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr3_spectratype_no_outliers.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr4_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr2_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/composition_logos/CDR2/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/CDR1/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/CDR3/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/FR1/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/FR4/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/FR2/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/FR3/PCR1_cumulative_logo.csv
inst/extdata/ex/auxiliary/PCR1/diversity/composition_logos/FR3/PCR1_cumulative_logo_raw.csv
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr3_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr1_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_cdr3_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_v_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr2_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr4_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr1_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_fr2_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr3_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_v_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_cdr3_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr1_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_cdr2_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR1/annot/PCR1_all_clones_len_dist.csv
inst/extdata/ex/auxiliary/PCR1/annot/analysis.params
inst/extdata/ex/auxiliary/PCR1/annot/PCR1_all_clones_len_dist_no_outliers.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_productive.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igd_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_inframe_unproductive.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/analysis.params
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_productivity.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_vjframe_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_region_inframe.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igj_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igj_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_dist_in_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igd_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_region_outframe.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_start_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/analysis.params
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_gaps_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_mismatches_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_identity_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igd_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igd_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_vjassoc.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igj_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_bitscore_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igj_dist_family_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/PCR2/analysis.params
inst/extdata/ex/auxiliary/PCR2/summary.txt
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_duplication.csv
inst/extdata/ex/auxiliary/PCR2/diversity/analysis.params
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_fr_duplication.csv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_duplication.csv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/lower_bound_estimate.tsv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/diversity_indices.tsv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_v_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr3_spectratype_no_outliers.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr4_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr3_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/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/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/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/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/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/clonotypes/PCR2_cdr1_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr3_clonotypes_all_under.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_cdr3_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_fr1_clonotypes_all_under.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_v_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_fr4_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_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_v_clonotypes_all_over.csv.gz
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/annot/analysis.params
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_productive.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/analysis.params
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_vjframe_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_stopcodon_region_outframe.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_inframe_unproductive.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_igd_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_productivity.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_stopcodon_dist_in_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_stopcodon_region_inframe.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igj_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igd_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igj_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_gaps_hm.tsv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igj_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/analysis.params
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_start_hm.tsv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_identity_hm.tsv
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_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_vjassoc.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR3/analysis.params
inst/extdata/ex/auxiliary/PCR3/summary.txt
inst/extdata/ex/auxiliary/PCR3/diversity/analysis.params
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_duplication.csv
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_duplication.csv
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_duplication.csv
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/lower_bound_estimate.tsv
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/diversity_indices.tsv
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr3_spectratype_no_outliers.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_v_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr1_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr4_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr1_spectratype.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/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/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/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/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/clonotypes/PCR3_fr2_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr4_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_under.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr2_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr2_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr1_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr4_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr1_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr1_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr3_clonotypes_all_over.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_cdr2_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_v_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr3_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR3/annot/PCR3_all_clones_len_dist_no_outliers.csv
inst/extdata/ex/auxiliary/PCR3/annot/analysis.params
inst/extdata/ex/auxiliary/PCR3/annot/PCR3_all_clones_len_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igd_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igd_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_vjframe_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igj_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_productive.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_region_outframe.csv
inst/extdata/ex/auxiliary/PCR3/productivity/analysis.params
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igj_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_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_inframe_unproductive.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_dist_in_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_productivity.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_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_cdr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_bitscore_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igj_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/analysis.params
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_start_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_identity_hm.tsv
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_igd_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_gaps_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_vjassoc.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_mismatches_hm.tsv
inst/extdata/ex/hdf/README
vignettes/simulation_flowchart_full.jpg
vignettes/post_report_fs.png
vignettes/abseqR.Rmd
vignettes/abseq_workflow_MA.jpg
R/pairwise.R R/statistics.R R/util.R R/upstreamAnalysis.R R/abseqReport.R R/AbSeqCRep.R R/primerAnalysis.R R/diversityAnalysis.R R/annotationAnalysis.R R/plotter.R R/AbSeqRep.R R/abundanceAnalysis.R R/productivityAnalysis.R R/distributions.R R/accessors-AbSeq.R man/dot-generateReport.Rd man/dot-alignQualityHeatMaps.Rd man/plus-AbSeqCRep-AbSeqCRep-method.Rd man/dot-saveAs.Rd man/dot-asRepertoireUpstream.Rd man/dot-findRepertoires.Rd man/plus-AbSeqCRep-AbSeqRep-method.Rd man/dot-asRepertoireName.Rd man/dot-getTotal.Rd man/dot-asRepertoireSubjectStart.Rd man/dot-abundancePlot.Rd man/dot-capitalize.Rd man/plus-AbSeqRep-AbSeqCRep-method.Rd man/dot-plotPrimerIGVStatus.Rd man/dot-primerAnalysis.Rd man/dot-asRepertoirePrimer5.Rd man/dot-cloneDistHist.Rd man/dot-generateDelayedReport.Rd man/dot-abundanceAnalysis.Rd man/dot-plotRecapture.Rd man/dot-generateAllSpectratypes.Rd man/abseqReport.Rd man/dot-plotUpstreamLength.Rd man/dot-asRepertoireQueryStart.Rd man/dot-asRepertoireBitscore.Rd man/dot-asRepertoireDir.Rd man/dot-plotDist.Rd man/plus-AbSeqRep-AbSeqRep-method.Rd man/dot-readSummary.Rd man/dot-asRepertoireList.Rd man/dot-canonicalizeTitle.Rd man/dot-diversityAnalysis.Rd man/dot-productivityAnalysis.Rd man/dot-asRepertoireAlignLen.Rd man/dot-loadMatrixFromDF.Rd man/dot-substituteStringInFile.Rd man/dot-annotAnalysis.Rd man/dot-checkVert.Rd man/dot-summarySE.Rd man/dot-plotRarefaction.Rd man/dot-calculateDInd.Rd man/dot-aminoAcidBar.Rd man/dot-asRepertoireChain.Rd man/dot-plotDuplication.Rd man/dot-UTR5Analysis.Rd man/dot-reportLBE.Rd man/report.Rd man/dot-prodDistPlot.Rd man/dot-plotErrorDist.Rd man/AbSeqCRep-class.Rd man/dot-plotSpectratype.Rd man/dot-loadSamplesFromString.Rd man/dot-scatterPlot.Rd man/dot-plotIGVUpstreamLenDistDetailed.Rd man/dot-getLineTypes.Rd man/dot-vennIntersection.Rd man/dot-correlationTest.Rd man/dot-plotPrimerIntegrity.Rd man/dot-secretionSignalAnalysis.Rd man/dot-calculateDiversityEstimates.Rd man/dot-plotCirclize.Rd man/dot-plotIGVErrors.Rd man/dot-commonPrimerNames.Rd man/AbSeqRep-class.Rd man/dot-clonotypeAnalysis.Rd man/dot-pairwiseComparison.Rd man/dot-cloneDistMarginal.Rd man/dot-boxPlot.Rd man/dot-scatterPlotComplex.Rd man/dot-emptyPlot.Rd man/dot-allPrimerNames.Rd man/dot-distanceMeasure.Rd man/dot-productivityPlot.Rd man/dot-hmFromMatrix.Rd man/dot-plotIGVUpstreamLenDist.Rd man/dot-plotSamples.Rd man/dot-asRepertoirePrimer3.Rd man/dot-regionAnalysis.Rd man/dot-collateReports.Rd man/dot-plotDiversityCurves.Rd man/dot-analyzeUpstreamValidity.Rd man/dot-aminoAcidPlot.Rd man/dot-plotUpstreamLengthDist.Rd man/dot-inferAnalyzed.Rd man/dot-topNDist.Rd
man/figures/README
build/vignette.rds
tests/testthat.R tests/testthat/test_AbSeqCRep.R tests/testthat/test_report.R tests/testthat/test_AbSeqRep.R tests/testthat/test_abseqReport.R
abseqR documentation built on Nov. 1, 2018, 4:34 a.m.