Package index • cailab.utils

BioCyc Database

Functions for interacting with BioCyc database

biocyc_add_property_column(): 给 BioCyc SmartTable 添加属性列

biocyc_create_smart_table(): 创建 BioCyc SmartTable

biocyc_delete_smart_table(): 删除BioCyc SmartTable

biocyc_enrichment(): BioCyc 富集分析

biocyc_get_all(): 获取所有数据

biocyc_get_enrichment_result(): 获取富集分析结果

biocyc_retrieve_smart_table() biocyc_get_smart_table(): 检索 BioCyc SmartTable

biocyc_session(): 建立BioCyc会话

biocyc_transform(): Convert BioCyc SmartTable

properties: BioCyc 数据库属性说明

transformations: BioCyc 服务可用转换类型

Bibliometric Analysis

Functions for bibliometric analysis and visualization

get_doi_record(): 从 doi.org 获取文献引用信息

get_pubmed_record(): 从 PubMed 获取文献记录

insert_citation(): Insert Citation

read_fast5k(): 读取 WebofScience 导出的 Fast5000 文件

Sequence Analysis

Functions for sequence alignment and analysis

design_specific_primer(): Design specific primer

run_alignment_with_muscle(): Run multiple sequence alignment with MUSCLE

tree_from_aln(): Construct a phylogenetic tree from sequence alignment

Synthetic Community

Functions for synthetic community analysis

combinations(): Get all possible combinations of n sets

one_plate(): The composition of community in a 8x8 plate (64 SynComs)

sort_combination(): Sort combination in a string

sub_community(): Find n depth children of a synthetic community

Data Visualization

Functions for data visualization and plotting

plot_tree(): Plot tree with ggtree

DT_output(): Use DT to output a tibble

DT_table(): A table generated by DT::datatable() with button to export data

extract_from_hist_graph(): Filter data.frame by graph nodes

four_dimension_barplot(): Show four tags of a bibliometrix data.frame

gg_boxplot(): boxplot

gg_boxplot_with_group(): Plot a boxplot and add group to it

ggpie(): plot pie chart for table or vector

kable_classic2(): A table generated by kableExtra

tableTag(): Count items in characters

tableTag_barplot(): tableTag downstream plot

Network Analysis

Functions for network analysis and visualization

graph_add_node_pagerank() graph_add_node_degree(): Modification of igraph Object

simplified_network() country_network() author_network() university_network() keyword_network(): Construct Networks of Different Tags

R Markdown Utilities

Functions for R Markdown document processing

rnw2rmd(): Convert vignettes from Rnw to Rmd

figure_caption_link(): Show the download links of figures when multiple devices are used

Video Summary

Functions for video content processing and summarization

yt_playlist_title(): 获取播放列表标题

yt_sub_clean(): 解析字幕文件

yt_sub_download(): 下载 YouTube 视频字幕

yt_summarize_video(): 处理单个视频并生成摘要

yt_summary(): 一键生成 YouTube 视频摘要

yt_video_title(): 获取视频标题

AI Integration

Functions for integrating with AI services

zhipuai_batch_build(): 构建智谱AI批处理任务

zhipuai_batch_create() zhipuai_batch_submit(): 创建批处理任务

zhipuai_batch_list(): 列出 Batch 任务

zhipuai_batch_list_all(): 迭代获取所有 Batch 任务

zhipuai_batch_results_download(): 下载 Batch 批处理任务的结果

zhipuai_batch_results_parse(): 解析智谱AI批处理任务的结果文件

zhipuai_batch_status_check(): 持续检查批处理任务的状态

zhipuai_batch_status_get(): 检查 Batch 批处理任务的状态

zhipuai_file_delete(): 删除文件

zhipuai_file_download(): 下载智谱AI平台上的文件

zhipuai_file_upload(): 上传文件到智谱AI平台

zhipuai_result_chat_parser(): 解析智谱 AI 任务结果中的聊天任务结果

zhipuai_result_embedding_parser(): 解析智谱 AI 任务结果中的嵌入任务结果

baidu_segment(): Use Baidu Cloud word segmentation service

get_gpt4_response(): 获取 GPT-4 响应

gpt_text_summary(): 生成视频摘要

Helper Functions

Utility functions and helpers

install_missing_packages(): Install missing package and retry

is_child(): Test whether community a is the subset of community b

is_relative(): Test whether community a is the relative of community b

paste2(): Paste which can ignore NA and empty strings

print_git_log(): Print git log in datatable

set_proxy(): Set http(s) proxy in the current R session

git_add_multiple_push_remote() git_delete_push_remote() git_show_remote_origin(): Setup git remote push urls

tag_by_regex(): Tag record by regular expression search

type_of_id(): 判断 ID 的类型

var2header(): Remove specific connector in string