Files in malhamdoosh/abseqR
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
Makefile
NAMESPACE
NEWS
R/AbSeqCRep.R
R/AbSeqRep.R
R/abseqReport.R
R/abundanceAnalysis.R
R/accessors-AbSeq.R
R/annotationAnalysis.R
R/distributions.R
R/diversityAnalysis.R
R/pairwise.R
R/plotter.R
R/primerAnalysis.R
R/productivityAnalysis.R
R/statistics.R
R/upstreamAnalysis.R
R/util.R
README.md
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_igd_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igj_dist_family_level.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_igv_align_quality_gaps_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_identity_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_mismatches_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_align_quality_start_hm.tsv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/abundance/PCR1_vjassoc.csv
inst/extdata/ex/auxiliary/PCR1/abundance/analysis.params
inst/extdata/ex/auxiliary/PCR1/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/annot/analysis.params
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_duplication.csv
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_v_duplication.csv
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_cdr_v_rarefaction.csv.gz
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/PCR1_fr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/PCR1_fr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/analysis.params
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_cdr2_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_cdr3_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_fr1_clonotypes_all_over.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_over.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr2_clonotypes_all_under.csv.gz
inst/extdata/ex/auxiliary/PCR1/diversity/clonotypes/PCR1_fr3_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_fr4_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_v_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/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/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/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/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/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/diversity_indices.tsv
inst/extdata/ex/auxiliary/PCR1/diversity/lower_bound_estimate.tsv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr1_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_cdr3_spectratype_no_outliers.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_fr1_spectratype.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_fr4_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/diversity/spectratypes/PCR1_v_spectratype.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr2_gaps_dist_out_of_frame.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_cdr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_cdr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_fr3_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_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igd_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igd_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igj_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igj_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_inframe_unproductive.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_dist_productive.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_productivity.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_dist_in_frame.csv
inst/extdata/ex/auxiliary/PCR1/productivity/PCR1_stopcodon_region_inframe.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/productivity/analysis.params
inst/extdata/ex/auxiliary/PCR1/summary.txt
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igd_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igj_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igj_dist_variant_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_gaps_hm.tsv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_identity_hm.tsv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_align_quality_mismatches_hm.tsv
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_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_dist_variant_level.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_igv_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/abundance/PCR2_vjassoc.csv
inst/extdata/ex/auxiliary/PCR2/abundance/analysis.params
inst/extdata/ex/auxiliary/PCR2/analysis.params
inst/extdata/ex/auxiliary/PCR2/annot/PCR2_all_clones_len_dist.csv
inst/extdata/ex/auxiliary/PCR2/annot/PCR2_all_clones_len_dist_no_outliers.csv
inst/extdata/ex/auxiliary/PCR2/annot/analysis.params
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_duplication.csv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_duplication.csv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_cdr_v_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_duplication.csv
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/PCR2_fr_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/analysis.params
inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr1_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr1_clonotypes_all_under.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_cdr3_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR2/diversity/clonotypes/PCR2_cdr3_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_fr1_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_fr2_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_fr3_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_v_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/composition_logos/CDR1/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/CDR2/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/CDR3/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/FR1/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/FR2/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/FR3/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/FR4/PCR2_cumulative_logo.csv
inst/extdata/ex/auxiliary/PCR2/diversity/composition_logos/FR4/PCR2_cumulative_logo_raw.csv
inst/extdata/ex/auxiliary/PCR2/diversity/diversity_indices.tsv
inst/extdata/ex/auxiliary/PCR2/diversity/lower_bound_estimate.tsv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr1_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_cdr3_spectratype_no_outliers.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr1_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_fr4_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/diversity/spectratypes/PCR2_v_spectratype.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_cdr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_fr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igd_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igd_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igj_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igj_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_inframe_unproductive.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_igv_dist_out_of_frame.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_igv_mismatches_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_stopcodon_region_outframe.csv
inst/extdata/ex/auxiliary/PCR2/productivity/PCR2_vjframe_dist.csv
inst/extdata/ex/auxiliary/PCR2/productivity/analysis.params
inst/extdata/ex/auxiliary/PCR2/summary.txt
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igd_dist_gene_level.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_align_quality_bitscore_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_gaps_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_identity_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_mismatches_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_align_quality_start_hm.tsv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_family_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_gene_level.csv
inst/extdata/ex/auxiliary/PCR3/abundance/PCR3_igv_dist_variant_level.csv
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_vjassoc.csv
inst/extdata/ex/auxiliary/PCR3/abundance/analysis.params
inst/extdata/ex/auxiliary/PCR3/analysis.params
inst/extdata/ex/auxiliary/PCR3/annot/PCR3_all_clones_len_dist.csv
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/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/PCR3_cdr_v_duplication.csv
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_rarefaction.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_cdr_v_recapture.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/PCR3_fr_duplication.csv
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/analysis.params
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_cdr1_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_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_over.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_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_fr2_clonotypes_all_over.csv.gz
inst/extdata/ex/auxiliary/PCR3/diversity/clonotypes/PCR3_fr2_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_fr3_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_fr4_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_v_clonotypes_all_under.csv.gz
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/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/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/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/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/diversity_indices.tsv
inst/extdata/ex/auxiliary/PCR3/diversity/lower_bound_estimate.tsv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr1_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr2_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr3_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_cdr3_spectratype_no_outliers.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_fr1_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_fr4_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/diversity/spectratypes/PCR3_v_spectratype.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr2_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_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_cdr3_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr1_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_gaps_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr2_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_fr3_gaps_dist.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_igd_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igd_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igj_gaps_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igj_mismatches_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_inframe_unproductive.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_out_of_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_igv_dist_productive.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_productivity.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_dist_in_frame.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_region_inframe.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_stopcodon_region_outframe.csv
inst/extdata/ex/auxiliary/PCR3/productivity/PCR3_vjframe_dist.csv
inst/extdata/ex/auxiliary/PCR3/productivity/analysis.params
inst/extdata/ex/auxiliary/PCR3/summary.txt
inst/extdata/ex/hdf/README
inst/extdata/index.Rmd
inst/extdata/template.Rmd
inst/script/ex.md
inst/script/index.txt
inst/script/template.txt
man/AbSeqCRep-class.Rd
man/AbSeqRep-class.Rd
man/abseqReport.Rd
man/dot-UTR5Analysis.Rd
man/dot-abundanceAnalysis.Rd
man/dot-abundancePlot.Rd
man/dot-alignQualityHeatMaps.Rd
man/dot-allPrimerNames.Rd
man/dot-aminoAcidBar.Rd
man/dot-aminoAcidPlot.Rd
man/dot-analyzeUpstreamValidity.Rd
man/dot-annotAnalysis.Rd
man/dot-asRepertoireAlignLen.Rd
man/dot-asRepertoireBitscore.Rd
man/dot-asRepertoireChain.Rd
man/dot-asRepertoireDir.Rd
man/dot-asRepertoireList.Rd
man/dot-asRepertoireName.Rd
man/dot-asRepertoirePrimer3.Rd
man/dot-asRepertoirePrimer5.Rd
man/dot-asRepertoireQueryStart.Rd
man/dot-asRepertoireSubjectStart.Rd
man/dot-asRepertoireUpstream.Rd
man/dot-boxPlot.Rd
man/dot-calculateDInd.Rd
man/dot-calculateDiversityEstimates.Rd
man/dot-canonicalizeTitle.Rd
man/dot-capitalize.Rd
man/dot-checkVert.Rd
man/dot-cloneDistHist.Rd
man/dot-cloneDistMarginal.Rd
man/dot-clonotypeAnalysis.Rd
man/dot-collateReports.Rd
man/dot-commonPrimerNames.Rd
man/dot-correlationTest.Rd
man/dot-distanceMeasure.Rd
man/dot-diversityAnalysis.Rd
man/dot-emptyPlot.Rd
man/dot-findRepertoires.Rd
man/dot-generateAllSpectratypes.Rd
man/dot-generateDelayedReport.Rd
man/dot-generateReport.Rd
man/dot-getLineTypes.Rd
man/dot-getTotal.Rd
man/dot-hmFromMatrix.Rd
man/dot-inferAnalyzed.Rd
man/dot-loadMatrixFromDF.Rd
man/dot-loadSamplesFromString.Rd
man/dot-pairwiseComparison.Rd
man/dot-plotCirclize.Rd
man/dot-plotDist.Rd
man/dot-plotDiversityCurves.Rd
man/dot-plotDuplication.Rd
man/dot-plotErrorDist.Rd
man/dot-plotIGVErrors.Rd
man/dot-plotIGVUpstreamLenDist.Rd
man/dot-plotIGVUpstreamLenDistDetailed.Rd
man/dot-plotPrimerIGVStatus.Rd
man/dot-plotPrimerIntegrity.Rd
man/dot-plotRarefaction.Rd
man/dot-plotRecapture.Rd
man/dot-plotSamples.Rd
man/dot-plotSpectratype.Rd
man/dot-plotUpstreamLength.Rd
man/dot-plotUpstreamLengthDist.Rd
man/dot-primerAnalysis.Rd
man/dot-prodDistPlot.Rd
man/dot-productivityAnalysis.Rd
man/dot-productivityPlot.Rd
man/dot-readSummary.Rd
man/dot-regionAnalysis.Rd
man/dot-reportLBE.Rd
man/dot-saveAs.Rd
man/dot-scatterPlot.Rd
man/dot-scatterPlotComplex.Rd
man/dot-secretionSignalAnalysis.Rd
man/dot-substituteStringInFile.Rd
man/dot-summarySE.Rd
man/dot-topNDist.Rd
man/dot-vennIntersection.Rd
man/figures/README
man/figures/abseq_gif.gif
man/plus-AbSeqCRep-AbSeqCRep-method.Rd
man/plus-AbSeqCRep-AbSeqRep-method.Rd
man/plus-AbSeqRep-AbSeqCRep-method.Rd
man/plus-AbSeqRep-AbSeqRep-method.Rd
man/report.Rd
tests/testthat.R
tests/testthat/test_AbSeqCRep.R
tests/testthat/test_AbSeqRep.R
tests/testthat/test_abseqReport.R
tests/testthat/test_report.R
vignettes/abseqR.Rmd
vignettes/abseq_workflow_MA.jpg
vignettes/post_report_fs.png
vignettes/simulation_flowchart_full.jpg
