diff --git a/DESCRIPTION b/DESCRIPTION index bc210ed..2c09d15 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,6 +8,7 @@ Maintainer: Thomas Rauter Description: Timeseries analysis of omics data can be carried out by fitting spline curves to the data and using limma for hypothesis testing. For this, the right spline freedom and further hyperparameters must be identified, and the obtained hits clustered based on the spline shape.The R package splinetime streamlines this whole process and generates reports. Depends: R (>= 4.3.0) License: MIT + file LICENSE +URL: https://csbg.github.io/SplineOmics Imports: ComplexHeatmap(>= 2.18.0), base64enc(>= 0.1-3), diff --git a/Meta/vignette.rds b/Meta/vignette.rds index cb2613e..2083dcf 100755 Binary files a/Meta/vignette.rds and b/Meta/vignette.rds differ diff --git a/README.Rmd b/README.Rmd index 1499b2b..c095f06 100755 --- a/README.Rmd +++ b/README.Rmd @@ -210,18 +210,7 @@ An explanation of the three different `limma` results is [here](https://csbg.git #### RNA-seq data -Transcriptomics data must be preprocessed for `limma`. You need to provide an -appropriate object, such as a `voom` object, in the `rna_seq_data` argument of -the `SplineOmics` object (see -[documentation](https://csbg.github.io/SplineOmics/reference/create_splineomics.html)). -Along with this, the normalized matrix -(e.g., the `$E` slot of the `voom` object) must be passed to the `data` -argument. This allows flexibility in preprocessing; you can use any method -you prefer as long as the final object and matrix are compatible with limma. -One way to preprocess your RNA-seq data is by using the `preprocess_rna_seq_data()` -function included in the `SplineOmics` package -(see [documentation](https://csbg.github.io/SplineOmics/reference/preprocess_rna_seq_data.html)). - +Transcriptomics data must be preprocessed for `limma`. You need to provide an appropriate object, such as a `voom` object, in the `rna_seq_data` argument of the `SplineOmics` object (see [documentation](https://csbg.github.io/SplineOmics/reference/create_splineomics.html)). Along with this, the normalized matrix (e.g., the `$E` slot of the `voom` object) must be passed to the `data` argument. This allows flexibility in preprocessing; you can use any method you prefer as long as the final object and matrix are compatible with limma. One way to preprocess your RNA-seq data is by using the `preprocess_rna_seq_data()` function included in the `SplineOmics` package (see [documentation](https://csbg.github.io/SplineOmics/reference/preprocess_rna_seq_data.html)). #### Glycan fractional abundance data diff --git a/doc/Docker_permission_denied.R b/doc/Docker_permission_denied.R old mode 100755 new mode 100644 diff --git a/doc/Docker_permission_denied.Rmd b/doc/Docker_permission_denied.Rmd index 142c38c..509b89a 100755 --- a/doc/Docker_permission_denied.Rmd +++ b/doc/Docker_permission_denied.Rmd @@ -1,10 +1,10 @@ --- -title: "Docker permission denied" +title: "Docker_permission_denied" author: "Thomas Rauter" date: "10 June, 2024" output: rmarkdown::html_vignette vignette: > - %\VignetteIndexEntry{Docker-permission-denied} + %\VignetteIndexEntry{Docker_permission_denied} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- @@ -18,7 +18,7 @@ knitr::opts_chunk$set( If you face 'permission denied' issues, you might need to add your user to the Docker group. Follow these steps: -**1. Create the Docker Group (if it doesn't already exist):** +**1. Create the Docker Group (if it doesn't already exist):** ``` sh sudo groupadd docker @@ -26,7 +26,7 @@ sudo groupadd docker This command creates a Docker group if it does not already exist on your system. -**2. Add Your User to the Docker Group:** +**2. Add Your User to the Docker Group:** ``` sh sudo usermod -aG docker $USER @@ -34,7 +34,7 @@ sudo usermod -aG docker $USER This command adds your user to the Docker group, which allows you to run Docker commands without sudo. -**3. Log Out and Log Back In:** +**3. Log Out and Log Back In:** This step is necessary to apply the group membership changes. After logging back in, you should be able to run Docker commands without sudo. @@ -44,7 +44,7 @@ Alternatively, you can use the following command to apply the group changes imme newgrp docker ``` -**4. Verify Docker Permissions:** +**4. Verify Docker Permissions:** To check if the permission issue is resolved, run a simple Docker command: @@ -54,7 +54,7 @@ docker run hello-world If the command runs successfully, you have configured Docker correctly. -**5. Ensure Docker Service is Running:** +**5. Ensure Docker Service is Running:** If you still encounter issues, ensure that the Docker service is running: diff --git a/doc/Docker_permission_denied.html b/doc/Docker_permission_denied.html old mode 100755 new mode 100644 index 455da3b..ca113bb --- a/doc/Docker_permission_denied.html +++ b/doc/Docker_permission_denied.html @@ -13,7 +13,7 @@ -Docker permission denied +Docker_permission_denied - - - - + + + + + + + + + + + - Skip to contents + Skip to contents