Cell Marker doc example is broken

hermidalc commented 2 years ago

When I try to run https://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html#cell-marker I get the following error:

cell_marker_data <- vroom::vroom('http://bio-bigdata.hrbmu.edu.cn/CellMarker/download/Human_cell_markers.txt')
New names:                                                                                                                                                      
• `height="30"></td></tr><tr><td` -> `height="30"></td></tr><tr><td...9`
• `class="i"><span` -> `class="i"><span...10`
• `height="30"></td></tr><tr><td` -> `height="30"></td></tr><tr><td...14`
• `class="i"><span` -> `class="i"><span...15`
Rows: 0 Columns: 17
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: " "
chr (17): <html, xmlns="http://www.w3.org/1999/xhtml"><head><meta, http-equiv="Content-Type"content="text/html;, charset=utf-8"/><title>错误-访问被禁止</title><style...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

cells <- cell_marker_data %>%
  dplyr::select(cellName, geneID) %>%
  dplyr::mutate(geneID = strsplit(geneID, ', ')) %>%
  tidyr::unnest()
Error: invalid version specification ‘0.68’

huerqiang commented 2 years ago

It should be a network problem. You can download Human_cell_markers.txt first, and then run cell_marker_data <- vroom::vroom(Your_path_to_Human_cell_markers.txt)

hermidalc commented 2 years ago

It should be a network problem. You can download Human_cell_markers.txt first, and then run cell_marker_data <- vroom::vroom(Your_path_to_Human_cell_markers.txt)

Doesn't work, when I wget the path or try via web browser the resulting data is an HTML page with a few Chinese characters.

hermidalc commented 2 years ago

Also, do you have Cell Marker data for mouse?

huerqiang commented 2 years ago

I just downloaded this file and it works well. Human_cell_markers.txt

huerqiang commented 2 years ago

You may need to try other download tools. I downloaded it using the Thunder(迅雷 for Chinese).

GuangchuangYu commented 1 year ago

A new version is provided in #21.

YuLab-SMU / biomedical-knowledge-mining-book

Cell Marker doc example is broken #17