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pull main #140

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Jul 30, 2024
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pull main #140

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6564e93
Merge pull request #138 from BIMSBbioinfo/dev
Artur-man Jul 26, 2024
1ffe619
fix import tutorial
Artur-man Jul 26, 2024
a45d704
Merge pull request #139 from Artur-man/main
Artur-man Jul 26, 2024
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2 changes: 1 addition & 1 deletion docs/importingdata.Rmd
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Expand Up @@ -421,7 +421,7 @@ Assays: OpenST(Main)
<img width="70%" height="70%" src="https://bimsbstatic.mdc-berlin.de/landthaler/VoltRon/Package/images/dbitseq_summary.jpg" class="center">
<p style="margin-left:3.4cm; margin-top:0.2cm; font-size:80%;"> <em> Image Credit: https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8 </em> </p>

We use the **importDBITSeq** function to import the OpenST [https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8](https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8) readouts and create a VoltRon object. The default path to the rna count matrix is accompanied by the path to the protein count matrix, which is optional. The **size** parameter here determines the size of each square pixel on the DBIT-Seq slide (default is 10$\mu$m).
We use the **importDBITSeq** function to import the DBIT-Seq [https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8](https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8) readouts and create a VoltRon object. The default path to the rna count matrix is accompanied by the path to the protein count matrix, which is optional. The **size** parameter here determines the size of each square pixel on the DBIT-Seq slide (default is 10$\mu$m).

We use the example with developing eye field in a E10 mouse embryo using 10-μm microfluidic (sample id: 0719cL for RNA, and 0719aL for Protein) channels that is deposited to NCBI/GEO ([GSE137986](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137986)).

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2 changes: 1 addition & 1 deletion docs/importingdata.html
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Expand Up @@ -908,7 +908,7 @@ <h2>DBIT-Seq</h2>
</em>
</p>
<p>We use the <strong>importDBITSeq</strong> function to import the
OpenST <a
DBIT-Seq <a
href="https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8">https://www.cell.com/cell/fulltext/S0092-8674(20)31390-8</a>
readouts and create a VoltRon object. The default path to the rna count
matrix is accompanied by the path to the protein count matrix, which is
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