Differences

This shows you the differences between two versions of the page.

--- upload_your_data [2016/03/23 11:19]
fsalavert
+++ upload_your_data [2020/04/03 20:18] (current)
@@ Line 1: / Line 1: @@
 ====== Upload your data ======
 Follow the following steps to upload your data to **HiPathia**.
-{{ :hipathia_upload1.png?600 |}}
+{{ :hipathia_upload1_5.png?600 |}}
 **1-** Either select the //My data// button in the upper bar of the HiPathia web or the //File browser// option of each pathway tool.
@@ Line 14: / Line 12: @@
 **3-** Select the folder in which you want to upload your data by navigating through your folders. Press the //Upload// button in the upper part of the folder you have selected. A window will appear.
-{{ :hipathia_upload2.png?600 |}}
+{{ :hipathia_upload2_5_1.png?600 |}}
-**4-** Indicate the type of the data you are about to upload by selecting the appropriate Bioformat in the //Upload file// window. If you are accessing this window from the //File browser// button of a tool form, then only the necessary bioformat will be showed. Bioformat names are self-explanatory.
+**4-** Click on the //Choose file// button and select the data file from your computer by navigating through your local files.
-  * **Data matrix expression**: File containing the an expression matrix, where each column is a sample of the experiment and each row the expression of a particular gene. For an example see {{:brca_genes_vals_bn.txt|}}. The format must be text (Tab delimited). If you are using excel please check [[https://support.office.com/en-us/article/Import-or-export-text-txt-or-csv-files-e8ab9ff3-be8d-43f1-9d52-b5e8a008ba5c#bmexport|this]].
+**5-** Indicate the type of the data you are about to upload by selecting the appropriate Data type in the //Upload file// window. If you are accessing this window from the //File browser// button of a tool form, then only the necessary Data type will be showed. Data-type names are self-explanatory.
-  * **Variant (VCF)**: Variant Call Format (VCF) file containing the variant information of a sample. For further information see the [[https://vcftools.github.io/specs.html|VCF specifications]].
+  * **Data matrix expression**: File containing an expression matrix, where each column is a sample of the experiment and each row the expression of a particular gene. For an example see {{:brca_genes_vals_bn.txt|}}. The format must be a **text tab delimited** file also called **[[https://en.wikipedia.org/wiki/Tab-separated_values|tsv]]** . If you are using excel please check [[https://support.office.com/en-us/article/Import-or-export-text-txt-or-csv-files-e8ab9ff3-be8d-43f1-9d52-b5e8a008ba5c#bmexport|this]].\\ The web version of Hipathia is limited to a maximum of 500 samples per dataset. For bigger datasets please use [[http://bioconductor.org/packages/release/bioc/html/hipathia.html|the R Bioconductor Hipathia package]]
+  * **Experimental design**: Two-columns file containing experimental information of each sample. The first column includes the names of the samples, the second column either the class to which each sample belongs or the value of an experimental variable. For an example see {{:brca_normal-basal_ed.txt|}}. The format must be a **text tab delimited** file also called **[[https://en.wikipedia.org/wiki/Tab-separated_values|tsv]]** . If you are using excel please check [[https://support.office.com/en-us/article/Import-or-export-text-txt-or-csv-files-e8ab9ff3-be8d-43f1-9d52-b5e8a008ba5c#bmexport|this]].
+  * **Gene List**: is Tab-separated values file. This file has just one column, that is the Entrez ID of genes (1 Entrez ID per line).
-  * **Experimental design**: Two-columns file containing experimental information of each sample. The first column includes the names of the samples, the second column either the class to which each sample belongs or the value of an experimental variable. For an example see {{:brca_normal-basal_ed.txt|}}. The format must be text (Tab delimited). If you are using excel please check [[https://support.office.com/en-us/article/Import-or-export-text-txt-or-csv-files-e8ab9ff3-be8d-43f1-9d52-b5e8a008ba5c#bmexport|this]].
+**6-** Select the //Upload// button and your data will be upload.
+===== Video tutorial  =====
+{{::uploaddata.mp4?900|}}
-**5-** Click on the //Choose file// button and select the data file from your computer by navigating through your local files.
-**6-** Select the //Upload// button and your data will be upload.

CoV-HiPathia

User Tools

Site Tools

Differences

Page Tools