From 10e2146da8a2c9cb80ee5b3326b1c4174083e9ab Mon Sep 17 00:00:00 2001 From: vivekbhr Date: Sun, 25 Feb 2024 21:47:45 +0100 Subject: [PATCH] fix docs references --- .readthedocs.yml | 1 + docs/content/tutorials.rst | 4 ++-- docs/content/tutorials/sincei_tutorial_10x.rst | 2 +- docs/content/tutorials/snmCATseq_glmPCA_analysis.ipynb | 2 +- docs/content/tutorials/snmCATseq_preprocessing.ipynb | 4 +++- 5 files changed, 8 insertions(+), 5 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 36b3ebe..f2c181e 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -14,3 +14,4 @@ python: path: . extra_requirements: - doc + - requirements: docs/requirements.txt diff --git a/docs/content/tutorials.rst b/docs/content/tutorials.rst index 8390de8..b4ba60c 100644 --- a/docs/content/tutorials.rst +++ b/docs/content/tutorials.rst @@ -17,5 +17,5 @@ Tutorials for using sincei inside python .. toctree:: :maxdepth: 1 - tutorials/snmC2Tseq_preprocessing - tutorials/GLM_PCA_analysis + tutorials/snmCATseq_preprocessing + tutorials/snmCATseq_glmPCA_analysis diff --git a/docs/content/tutorials/sincei_tutorial_10x.rst b/docs/content/tutorials/sincei_tutorial_10x.rst index b03bd0b..75eb5e7 100644 --- a/docs/content/tutorials/sincei_tutorial_10x.rst +++ b/docs/content/tutorials/sincei_tutorial_10x.rst @@ -47,7 +47,7 @@ We will use the ``gex_possorted_bam.bam`` for gene-expression data and sincei. These files can also be produced as part of the ``cellranger count`` workflow for scRNA-seq or scATAC-seq data alone. For convenience, we provide a subset of this data (only chromosome 2) -`here <>`__ +`here` .. code:: bash diff --git a/docs/content/tutorials/snmCATseq_glmPCA_analysis.ipynb b/docs/content/tutorials/snmCATseq_glmPCA_analysis.ipynb index c838f99..402b9b9 100644 --- a/docs/content/tutorials/snmCATseq_glmPCA_analysis.ipynb +++ b/docs/content/tutorials/snmCATseq_glmPCA_analysis.ipynb @@ -46,7 +46,7 @@ "## Read data\n", "\n", "\n", - "Starting from the files provided in our [figshare repository](), the data needs to be first processed as demonstrated in \"snmCATseq_prepcessing.ipynb\". We here load the output.\n", + "Starting from the files provided in our figshare repository, the data needs to be first processed as demonstrated in \"snmCATseq_prepcessing.ipynb\". We here load the output.\n", "\n", "In order to confirm whether glmPCA results help in identifying clusters of cells, we shall also load the celltype metadata provided in the Supplementary table 5 of the original manuscript.\n" ] diff --git a/docs/content/tutorials/snmCATseq_preprocessing.ipynb b/docs/content/tutorials/snmCATseq_preprocessing.ipynb index 37aea2d..ddac624 100644 --- a/docs/content/tutorials/snmCATseq_preprocessing.ipynb +++ b/docs/content/tutorials/snmCATseq_preprocessing.ipynb @@ -18,7 +18,9 @@ "cell_type": "code", "execution_count": 1, "id": "988e257e-c523-4ead-af26-99a45177a79c", - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ "import os, tqdm, itertools, math\n",