-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathNAMESPACE
144 lines (143 loc) · 3.63 KB
/
NAMESPACE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
# Generated by roxygen2: do not edit by hand
export(align_DNA_fasta)
export(check_fasta)
export(check_file)
export(col_JS_divergence)
export(col_freq)
export(col_sub_abs)
export(count_snps_in_bins)
export(dds2counts)
export(df2JSD)
export(df2bits)
export(df2mat)
export(df2pfm)
export(df2ppm)
export(df2pwm)
export(encode_onehot)
export(ensembl_id_2_entrez)
export(ensembl_id_2_gene_name)
export(fasta2df)
export(fasta2pim)
export(filter_dds)
export(find_containing_bin)
export(gene_name_2_ensembl_id)
export(get_alphabet_palette)
export(get_hPTM_FC)
export(get_mouse_tissue_devel_tbl)
export(gimme_PSI_expr_corr)
export(gimme_expr_mat)
export(gimme_mart)
export(gimme_psi_mat)
export(grep_gene_expression)
export(grep_psi)
export(gtf_attributes_as_cols)
export(gtf_attributes_as_list)
export(guess_alphabet)
export(guess_species)
export(hallgrimskirkja_plot)
export(longest_common_prefix)
export(longest_most_abundant_common_suffix)
export(permutate_seq)
export(permutationz)
export(plotALLU_hPTM)
export(plotMA_hPTM)
export(plot_JSD_logo)
export(plot_best_corr_genes)
export(plot_bits_logo)
export(plot_corr_dist)
export(plot_corr_gene_expr_psi)
export(plot_corr_heatmap)
export(plot_hist_dPSI)
export(plot_mouse_tissue_devel)
export(plot_pwm_as_bars)
export(plot_pwm_as_hm)
export(plot_rmats_summary)
export(plot_rudimentary_JSD_logo)
export(plot_rudimentary_logo)
export(plot_samples_PSI)
export(print_seq_perm)
export(read_EpiProfile_histone_ratio)
export(read_bed)
export(read_gtf)
export(read_rmats)
export(read_rmats_summary)
export(read_vst_tbl)
export(renumber_logo_seq_breaks)
export(res2df)
export(save_counts)
export(save_df_gsea_list)
export(show_dds_counts_freq)
export(showme_PCA2D)
export(slop_bed)
export(test_regexes)
export(tidy_hPTMs)
export(tidy_vst_expr)
export(tidy_vst_psi)
import(Cairo)
import(DESeq2)
import(MetBrewer)
import(XICOR)
import(dplyr)
import(ggalluvial)
import(ggfittext)
import(ggplot2)
import(ggrepel)
import(patchwork)
import(stringr)
import(tibble)
import(tidyr)
importFrom(BiocGenerics,estimateSizeFactors)
importFrom(Biostrings,DNAStringSetList)
importFrom(Biostrings,lcprefix)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,writeXStringSet)
importFrom(DESeq2,normalizationFactors)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,listEnsemblArchives)
importFrom(biomaRt,useEnsembl)
importFrom(biomaRt,useMart)
importFrom(csaw,normOffsets)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,everything)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(forcats,fct_inorder)
importFrom(forcats,fct_reorder)
importFrom(ggrepel,geom_text_repel)
importFrom(ggseqlogo,geom_logo)
importFrom(ggseqlogo,make_col_scheme)
importFrom(gtools,permutations)
importFrom(matrixStats,rowVars)
importFrom(msa,msaConvert)
importFrom(msa,msaMuscle)
importFrom(readr,locale)
importFrom(readr,read_delim)
importFrom(readr,write_delim)
importFrom(rlang,as_function)
importFrom(scales,number_format)
importFrom(seqinr,dist.alignment)
importFrom(seqinr,read.fasta)
importFrom(stats,prcomp)
importFrom(stringr,str_extract)
importFrom(stringr,str_remove)
importFrom(stringr,str_split)
importFrom(tibble,as_tibble)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyselect,contains)
importFrom(vctrs,vec_fill_missing)