Merge pull request #14 from complextissue/dev

Bioconda installation in documentation and image alignment
complextissue · Sep 7, 2024 · d386a3a · d386a3a
2 parents eb987a1 + 09b6336
commit d386a3a
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diff --git a/docs/source/example.ipynb b/docs/source/example.ipynb
@@ -41,92 +41,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This example requires `pybiomart` which is installed together with `pytximport`. Providing a host is optional, for a list of available archives that correspond to Ensembl releases, please consult [https://www.ensembl.org/info/website/archives/index.html](https://www.ensembl.org/info/website/archives/index.html). By default, the transcript ids will be mapped to the `ensembl_gene_id` field. If you prefer to use gene names, choose `external_gene_name`. The first time you run this function, it may take a few seconds to download the data."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>transcript_id</th>\n",
-       "      <th>gene_id</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>ENST00000387314</td>\n",
-       "      <td>MT-TF</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>ENST00000389680</td>\n",
-       "      <td>MT-RNR1</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>ENST00000387342</td>\n",
-       "      <td>MT-TV</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>ENST00000387347</td>\n",
-       "      <td>MT-RNR2</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>ENST00000386347</td>\n",
-       "      <td>MT-TL1</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "     transcript_id  gene_id\n",
-       "0  ENST00000387314    MT-TF\n",
-       "1  ENST00000389680  MT-RNR1\n",
-       "2  ENST00000387342    MT-TV\n",
-       "3  ENST00000387347  MT-RNR2\n",
-       "4  ENST00000386347   MT-TL1"
-      ]
-     },
-     "execution_count": 1,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "from pytximport.utils import create_transcript_to_gene_map\n",
-    "\n",
-    "transcript_gene_map_human = create_transcript_to_gene_map(\n",
-    "    species=\"human\",\n",
-    "    host=\"http://may2024.archive.ensembl.org/\",\n",
-    "    target_field=\"external_gene_name\",\n",
-    ")\n",
-    "transcript_gene_map_human.head(5)"
+    "This example requires `pybiomart` which is installed together with `pytximport`. Providing a host is optional, for a list of available archives that correspond to Ensembl releases, please consult [https://www.ensembl.org/info/website/archives/index.html](https://www.ensembl.org/info/website/archives/index.html). By default, the transcript ids will be mapped to the `ensembl_gene_id` field. If you prefer to use gene names, choose `external_gene_name`. Be aware that not all proposed transcripts have been assigned a name yet and thus will not be included if you use gene names. The first time you run this function, it may take a few seconds to download the data."
    ]
   },
   {

diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -25,6 +25,15 @@ python3 -m pip install pytximport
 
 :::
 
+:::{tab-item} Bioconda
+Install `pytximport` from `Bioconda` using `mamba` or `conda`:
+
+```bash
+mamba install -c bioconda pytximport
+```
+
+:::
+
 :::{tab-item} GitHub
 Install `pytximport` from GitHub using `pip`: