API for immunarch
Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Global functions
.colourblind_discrete Source code
.colourblind_vector Source code
.detect_format Source code
.get_coltypes Source code
.make_names Source code
.postprocess Source code
.quant_column_choice Man page Source code
.rem_legend Source code
.rem_xlab Source code
.rem_ylab Source code
.remove.alleles Source code
.remove.ext Source code
.tweak_col Source code
.tweak_fill Source code
.which_recomb_type Source code
AA_PROP Man page
AA_TABLE Man page
AA_TABLE_REVERSED Man page
ATCHLEY Man page
GENE_SEGMENTS Man page
KIDERA Man page
aa_prop Man page
aa_properties Man page
aa_table Man page
add_class Man page Source code
add_pb Man page Source code
apply_asymm Man page Source code
apply_symm Man page Source code
atchley Man page
bunch_translate Man page Source code
chao1 Man page Source code
check_distribution Man page Source code
check_group_names Source code
clonal.prop Man page
clonal_proportion Man page Source code
clonal_space_homeostasis Man page Source code
clonality Man page
coding Man page Source code
cosine_sim Source code
cosine_sim.default Source code
cosine_sim.numeric Source code
cross_entropy Man page Source code
dXX Source code
dbAnnotate Man page Source code
dbLoad Man page Source code
default_scale_fun Source code
diversity_eco Man page Source code
downsample Source code
downsample_col Source code
entropy Man page Source code
fill_reads Source code
fill_vec Source code
fixVis Man page Source code
geneUsage Man page Source code
geneUsageAnalysis Man page Source code
gene_segments Man page
gene_stats Man page Source code
gene_usage_cor Source code
gene_usage_cosine Source code
gene_usage_js Source code
genes Man page
get.kmers Man page
getKmers Man page Source code
get_aliases Man page
get_genes Man page Source code
get_public_repertoire_names Source code
gini_coef Man page Source code
gini_simpson Man page Source code
group_from_metadata Man page Source code
has_class Man page Source code
hill_numbers Man page Source code
horn_index Source code
immdata Man page
immunarch_data_format Man page
immunr_data_format Man page
immunr_dbscan Man page Source code
immunr_hclust Man page Source code
immunr_kmeans Man page Source code
immunr_mds Man page Source code
immunr_pca Man page Source code
immunr_tsne Man page Source code
inc_overlap Man page Source code
inframes Man page Source code
inverse_simpson Man page Source code
jaccard_index Source code
jaccard_index.character Source code
jaccard_index.default Source code
js_div Man page Source code
kidera Man page
kl_div Man page Source code
kmer_profile Man page Source code
load_segments Source code
makeKmerTable Man page
matrixdiagcopy Man page Source code
morisita_index Source code
noncoding Man page Source code
num2bin Source code
num_shared_clonotypes Source code
outofframes Man page Source code
overlap_coef Source code
overlap_coef.character Source code
overlap_coef.default Source code
parse_10x_consensus Source code
parse_10x_filt_contigs Source code
parse_airr Source code
parse_archer Source code
parse_catt Source code
parse_imgt Source code
parse_immunarch Source code
parse_immunoseq Source code
parse_migec Source code
parse_migmap Source code
parse_mitcr Source code
parse_mixcr Source code
parse_repertoire Source code
parse_tcr Source code
parse_vdjtools Source code
process_col_argument Man page Source code
process_metadata_arguments Source code
properties Man page
pubRep Man page Source code
pubRepApply Man page Source code
pubRepFilter Man page Source code
pubRepStatistics Man page Source code
publicRepertoire Man page
publicRepertoireApply Man page
publicRepertoireFilter Man page
public_matrix Man page Source code
rare_proportion Man page Source code
rarefaction Man page Source code
rename_column Source code
repClonality Man page Source code
repDiversity Man page Source code
repExplore Man page Source code
repLoad Man page Source code
repOverlap Man page Source code
repOverlapAnalysis Man page Source code
repSample Man page Source code
repSave Man page Source code
resample Source code
resample_col Source code
return_families Source code
return_segments Source code
sample_clonotypes Source code
save_immunarch Source code
save_vdjtools Source code
scdata Man page
segments Man page
select_barcodes Man page Source code
select_clusters Man page
set_pb Man page Source code
spectratype Man page Source code
split_to_kmers Man page Source code
switch_type Man page Source code
theme_cleveland2 Source code
top Man page Source code
top_proportion Man page Source code
trackClonotypes Man page Source code
translate_bunch Man page
tversky_index Source code
tversky_index.character Source code
tversky_index.default Source code
vis Man page Source code
vis.immunr_chao1 Man page Source code
vis.immunr_clonal_prop Man page Source code
vis.immunr_dbscan Man page Source code
vis.immunr_div Man page Source code
vis.immunr_dxx Man page Source code
vis.immunr_dynamics Man page Source code
vis.immunr_exp_clones Man page Source code
vis.immunr_exp_count Man page Source code
vis.immunr_exp_len Man page Source code
vis.immunr_exp_vol Man page Source code
vis.immunr_gene_usage Man page Source code
vis.immunr_ginisimp Man page Source code
vis.immunr_gu_matrix Man page Source code
vis.immunr_hclust Man page Source code
vis.immunr_hill Man page Source code
vis.immunr_homeo Man page Source code
vis.immunr_inc_overlap Man page Source code
vis.immunr_invsimp Man page Source code
vis.immunr_kmeans Man page Source code
vis.immunr_kmer_profile_pfm Source code
vis.immunr_kmer_profile_ppm Source code
vis.immunr_kmer_profile_pwm Source code
vis.immunr_kmer_profile_self Source code
vis.immunr_kmer_table Man page Source code
vis.immunr_mds Man page Source code
vis.immunr_ov_matrix Man page Source code
vis.immunr_pca Man page Source code
vis.immunr_public_repertoire Man page Source code
vis.immunr_public_statistics Man page Source code
vis.immunr_rare_prop Source code
vis.immunr_rarefaction Man page Source code
vis.immunr_spectr Source code
vis.immunr_spectr_nogene Source code
vis.immunr_tail_prop Man page
vis.immunr_top_prop Man page Source code
vis.immunr_tsne Man page Source code
vis_bar Man page Source code
vis_bar_stacked Source code
vis_box Man page Source code
vis_circos Man page Source code
vis_heatmap Man page Source code
vis_heatmap2 Man page Source code
vis_hist Man page Source code
vis_immunr_kmer_profile_main Man page Source code
vis_public_clonotypes Man page Source code
vis_public_frequencies Man page Source code
vis_seqlogo Man page Source code
vis_textlogo Man page Source code
immunarch documentation built on July 7, 2021, 9:08 a.m.