From ae7e0a519c46799b1605f8c0c0dd943e948cf577 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Mon, 16 Dec 2024 10:37:41 -0500 Subject: [PATCH 1/6] Add table to readme with example modules --- analyses/README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/analyses/README.md b/analyses/README.md index 60d27fead..f28ea061f 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -2,3 +2,14 @@ This directory contains the [OpenScPCA analysis modules](https://openscpca.readt Each directory represents a single analysis module. Each module contains a `README.md` file with information on its scientific goals and how to run it. + +## Example modules + +Several modules are provided as examples for how to use certain frameworks in OpenScPCA: + +| Module name | Purpose +|-------------|--------- +| `hello-R` | Demonstrates an example structure of an R-based module +| `hello-python` | Demonstrates an example structure of a Python-based module +| `hello-cluster` | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) +| `seurat-conversion`| Provides notebooks demonstrating the use of functions related to converting SCE to Seurat objects in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/), which also includes functions to convert Ensembl ids to gene symbols \ No newline at end of file From b08752166b2b801b088cc2202b58c509f995fa15 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Fri, 20 Dec 2024 09:45:43 -0500 Subject: [PATCH 2/6] remove seurat conversion line from table --- analyses/README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/analyses/README.md b/analyses/README.md index f28ea061f..672172c7b 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -12,4 +12,3 @@ Several modules are provided as examples for how to use certain frameworks in Op | `hello-R` | Demonstrates an example structure of an R-based module | `hello-python` | Demonstrates an example structure of a Python-based module | `hello-cluster` | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) -| `seurat-conversion`| Provides notebooks demonstrating the use of functions related to converting SCE to Seurat objects in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/), which also includes functions to convert Ensembl ids to gene symbols \ No newline at end of file From bf190aa549823e711e3bb26d0bc68218c0effb40 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Fri, 20 Dec 2024 11:01:44 -0500 Subject: [PATCH 3/6] make module names links --- analyses/README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/analyses/README.md b/analyses/README.md index 672172c7b..aa3f68e51 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -9,6 +9,6 @@ Several modules are provided as examples for how to use certain frameworks in Op | Module name | Purpose |-------------|--------- -| `hello-R` | Demonstrates an example structure of an R-based module -| `hello-python` | Demonstrates an example structure of a Python-based module -| `hello-cluster` | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) +| [`hello-R`](hello-R/) | Demonstrates an example structure of an R-based module +| [`hello-python`](hello-python/) | Demonstrates an example structure of a Python-based module +| [`hello-cluster`](hello-cluster/) | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) From bccc2c39ad26d052dc0127b289d1e74fff7b0662 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Fri, 20 Dec 2024 11:02:32 -0500 Subject: [PATCH 4/6] try spacing --- analyses/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/analyses/README.md b/analyses/README.md index aa3f68e51..3b2b40c78 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -7,8 +7,8 @@ Each module contains a `README.md` file with information on its scientific goals Several modules are provided as examples for how to use certain frameworks in OpenScPCA: -| Module name | Purpose -|-------------|--------- +| Module name | Purpose +|----------------------------|--------- | [`hello-R`](hello-R/) | Demonstrates an example structure of an R-based module | [`hello-python`](hello-python/) | Demonstrates an example structure of a Python-based module | [`hello-cluster`](hello-cluster/) | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) From 17c91fc2863b301031c705106f2b7550eb1542fd Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Fri, 20 Dec 2024 11:04:43 -0500 Subject: [PATCH 5/6] revert 'try spacing' --- analyses/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/analyses/README.md b/analyses/README.md index 3b2b40c78..aa3f68e51 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -7,8 +7,8 @@ Each module contains a `README.md` file with information on its scientific goals Several modules are provided as examples for how to use certain frameworks in OpenScPCA: -| Module name | Purpose -|----------------------------|--------- +| Module name | Purpose +|-------------|--------- | [`hello-R`](hello-R/) | Demonstrates an example structure of an R-based module | [`hello-python`](hello-python/) | Demonstrates an example structure of a Python-based module | [`hello-cluster`](hello-cluster/) | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) From fa1c68d62813c1f1985504970f436c4fc9693485 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Fri, 20 Dec 2024 11:20:40 -0500 Subject: [PATCH 6/6] Update analyses/README.md Co-authored-by: Joshua Shapiro --- analyses/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/analyses/README.md b/analyses/README.md index aa3f68e51..ee64bedb7 100644 --- a/analyses/README.md +++ b/analyses/README.md @@ -11,4 +11,4 @@ Several modules are provided as examples for how to use certain frameworks in Op |-------------|--------- | [`hello-R`](hello-R/) | Demonstrates an example structure of an R-based module | [`hello-python`](hello-python/) | Demonstrates an example structure of a Python-based module -| [`hello-cluster`](hello-cluster/) | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/) +| [`hello-clusters`](hello-clusters/) | Provides notebooks demonstrating the use of clustering and cluster evaluations functions in the [`rOpenScPCA` package](https://github.com/AlexsLemonade/rOpenScPCA/)