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Update HGG subtyping (4/11) #108

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merged 10 commits into from
Oct 28, 2024
Merged

Update HGG subtyping (4/11) #108

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eab63e8
update HGG subtyping module
komalsrathi Jun 20, 2024
96f6848
cancer_group_short is HGG where molecular_subtype is PXA
komalsrathi Aug 16, 2024
8e5bf85
Merge branch 'master' into update-subtyping
naqvia Aug 16, 2024
0f42796
rerun
komalsrathi Aug 19, 2024
11f2753
rerun with fread fix
komalsrathi Aug 19, 2024
6b901e8
Merge remote-tracking branch 'origin/master' into update-subtyping
komalsrathi Aug 20, 2024
8e69b0a
add txdbmaker
komalsrathi Aug 20, 2024
51c1f93
Merge pull request #118 from d3b-center/update-dockerfile
komalsrathi Aug 21, 2024
8e4f096
Merge pull request #106 from d3b-center/update-nf1-score
komalsrathi Oct 28, 2024
c48d996
Merge remote-tracking branch 'origin/master' into update-subtyping
komalsrathi Oct 28, 2024
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10 changes: 5 additions & 5 deletions analyses/molecular-subtyping-HGG/00-fusion-summary.nb.html
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Expand Up @@ -1767,14 +1767,14 @@ <h3>Libraries and functions</h3>
<!-- rnb-source-begin eyJkYXRhIjoibGlicmFyeSh0aWR5dmVyc2UpIn0= -->
<pre class="r"><code>library(tidyverse)</code></pre>
<!-- rnb-source-end -->
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<pre><code>── Attaching core tidyverse packages ───────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
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<pre><code>── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ ggplot2 3.5.1 ✔ tibble 3.2.1
✔ lubridate 1.9.3 ✔ tidyr 1.3.1
✔ purrr 1.0.2
── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (&lt;http://conflicted.r-lib.org/&gt;) to force all conflicts to become errors</code></pre>
Expand Down Expand Up @@ -1845,9 +1845,9 @@ <h3>Read in data</h3>
#&#39; file but have been assayed - we will gather those from the histology file
hist &lt;- read_tsv(file.path(dataDir, &quot;Hope-GBM-histologies-base.tsv&quot;))</code></pre>
<!-- rnb-source-end -->
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<pre><code>Rows: 632 Columns: 94
── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: &quot;\t&quot;
chr (56): Kids_First_Biospecimen_ID, sample_id, Kids_First_Participant_ID, e...
dbl (29): aliquot_id, age_at_diagnosis_days, age_at_event_days, age_at_chemo...
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