mirror of
https://github.com/johrpan/ubigen.git
synced 2025-10-26 19:57:24 +01:00
Add screenshots to help page
This commit is contained in:
parent
a046ed67c4
commit
254c43b016
6 changed files with 13 additions and 0 deletions
BIN
inst/content/custom_genes.png
Normal file
BIN
inst/content/custom_genes.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 114 KiB |
BIN
inst/content/gene_selector.png
Normal file
BIN
inst/content/gene_selector.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 21 KiB |
BIN
inst/content/gsea.png
Normal file
BIN
inst/content/gsea.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 128 KiB |
|
|
@ -16,6 +16,8 @@ from a dropdown menu. To paste your genes as a whitespace separated list of
|
||||||
either HGNC symbols or Ensembl gene IDs (in the form `ENSG00000164362`), change
|
either HGNC symbols or Ensembl gene IDs (in the form `ENSG00000164362`), change
|
||||||
the top dropdown from "Select from list" to the desired input method.
|
the top dropdown from "Select from list" to the desired input method.
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
## Which information does the tool give for my genes of interest?
|
## Which information does the tool give for my genes of interest?
|
||||||
|
|
||||||
Once your genes have been selected, the user interface will automatically switch
|
Once your genes have been selected, the user interface will automatically switch
|
||||||
|
|
@ -33,6 +35,8 @@ their top right corner):
|
||||||
4. A detailed table (downloadable as CSV) including scores, ranks and
|
4. A detailed table (downloadable as CSV) including scores, ranks and
|
||||||
percentiles as well as the computed parameters for your genes.
|
percentiles as well as the computed parameters for your genes.
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
## How can I change the parameters of the method?
|
## How can I change the parameters of the method?
|
||||||
|
|
||||||
The panel on the left side offers multiple controls to change the parameters of
|
The panel on the left side offers multiple controls to change the parameters of
|
||||||
|
|
@ -46,6 +50,8 @@ as well as their weight contributing to that score. These are the criteria:
|
||||||
| Expression level | The median expression level (logarithmic) is determined for each gene across all samples. Alternatively, it is possible to select the mean expression. | 25% |
|
| Expression level | The median expression level (logarithmic) is determined for each gene across all samples. Alternatively, it is possible to select the mean expression. | 25% |
|
||||||
| Expression variation | Measure of the variation of a gene’s expression between samples. By default, the interquartile range (IQR) normalized by the median is used. Other options include the IQR itself, the standard deviation and the coefficient of variation. | -25% |
|
| Expression variation | Measure of the variation of a gene’s expression between samples. By default, the interquartile range (IQR) normalized by the median is used. Other options include the IQR itself, the standard deviation and the coefficient of variation. | -25% |
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
## What does the GSEA tab do?
|
## What does the GSEA tab do?
|
||||||
|
|
||||||
The "GSEA" tab provides a simple gene set enrichment analysis using
|
The "GSEA" tab provides a simple gene set enrichment analysis using
|
||||||
|
|
@ -54,6 +60,8 @@ of over-representation of annotated genes in the top part of the ranking which
|
||||||
is a way to insinuate the biological or at least scientific relevance of the
|
is a way to insinuate the biological or at least scientific relevance of the
|
||||||
scoring.
|
scoring.
|
||||||
|
|
||||||
|

|
||||||
|
|
||||||
## How can I perform analyses of ubiquity relative to my own expression dataset?
|
## How can I perform analyses of ubiquity relative to my own expression dataset?
|
||||||
|
|
||||||
Because of the computational requirements we can not publicly provide this
|
Because of the computational requirements we can not publicly provide this
|
||||||
|
|
|
||||||
BIN
inst/content/method_parameters.png
Normal file
BIN
inst/content/method_parameters.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 76 KiB |
|
|
@ -36,3 +36,8 @@ h5 {
|
||||||
.container td {
|
.container td {
|
||||||
padding: 4px;
|
padding: 4px;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.container img {
|
||||||
|
max-width: 100%;
|
||||||
|
height: auto;
|
||||||
|
}
|
||||||
Loading…
Add table
Add a link
Reference in a new issue