diff --git a/DESCRIPTION b/DESCRIPTION
index ec52917..097859c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dreamlet
 Type: Package
 Title: Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs
-Version: 1.4.0
+Version: 1.4.1
 Date: 2024-11-05
 Authors@R: person("Gabriel", "Hoffman", role=c("aut", "cre"), email="gabriel.hoffman@mssm.edu", comment=c(ORCID="0000-0002-0957-0224"))
 Description: Recent advances in single cell/nucleus transcriptomic technology has enabled collection of cohort-scale datasets to study cell type specific gene expression differences associated disease state, stimulus, and genetic regulation. The scale of these data, complex study designs, and low read count per cell mean that characterizing cell type specific molecular mechanisms requires a user-frieldly, purpose-build analytical framework. We have developed the dreamlet package that applies a pseudobulk approach and fits a regression model for each gene and cell cluster to test differential expression across individuals associated with a trait of interest. Use of precision-weighted linear mixed models enables accounting for repeated measures study designs, high dimensional batch effects, and varying sequencing depth or observed cells per biosample.
diff --git a/NEWS.md b/NEWS.md
index a2279a7..bc9edbd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,8 @@
 
+# dreamlet 1.4.0
+ - Nov 5, 2024
+ - update to Bioc 3.20
+
 # dreamlet 1.3.4
  - Oct 27, 2024
  - Better error reporting addressing https://github.com/GabrielHoffman/dreamlet/issues/25
diff --git a/docs/news/index.html b/docs/news/index.html
index 33e9213..f41d1df 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -40,6 +40,11 @@
       <small>Source: <a href="https://github.com/DiseaseNeurogenomics/dreamlet/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.4.0" id="dreamlet-140">dreamlet 1.4.0<a class="anchor" aria-label="anchor" href="#dreamlet-140"></a></h2>
+<ul><li>Nov 5, 2024</li>
+<li>update to Bioc 3.20</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.3.4" id="dreamlet-134">dreamlet 1.3.4<a class="anchor" aria-label="anchor" href="#dreamlet-134"></a></h2>
 <ul><li>Oct 27, 2024</li>
@@ -117,9 +122,9 @@ <h2 class="pkg-version" data-toc-text="1.1.16" id="dreamlet-1116">dreamlet 1.1.1
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.1.15" id="dreamlet-1115">dreamlet 1.1.15<a class="anchor" aria-label="anchor" href="#dreamlet-1115"></a></h2>
 <ul><li>Feb 5, 2024</li>
-<li>Fix bug in call to <code><a href="https://rdrr.io/pkg/limma/man/ebayes.html" class="external-link">eBayes()</a></code>
+<li>Fix bug in call to <code>eBayes()</code>
 </li>
-<li>in <code><a href="../reference/processAssays.html">processAssays()</a></code> pass argument <code>scaledByLib</code> to <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/voomWithDreamWeights.html" class="external-link">voomWithDreamWeights()</a></code>
+<li>in <code><a href="../reference/processAssays.html">processAssays()</a></code> pass argument <code>scaledByLib</code> to <code>voomWithDreamWeights()</code>
 </li>
 </ul></div>
     <div class="section level2">
@@ -213,7 +218,7 @@ <h2 class="pkg-version" data-toc-text="1.1.3" id="dreamlet-113">dreamlet 1.1.3<a
 <ul><li>Nov 22, 2023</li>
 <li>add <code><a href="../reference/stackAssays.html">stackAssays()</a></code>
 </li>
-<li>add <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/diffVar-method.html" class="external-link">diffVar()</a></code>
+<li>add <code>diffVar()</code>
 </li>
 <li>fix <code>getVarFromCounts)</code> so <code>zeta</code> is a mean, not a sum</li>
 </ul></div>
@@ -221,7 +226,7 @@ <h2 class="pkg-version" data-toc-text="1.1.3" id="dreamlet-113">dreamlet 1.1.3<a
 <h2 class="pkg-version" data-toc-text="1.1.2" id="dreamlet-112">dreamlet 1.1.2<a class="anchor" aria-label="anchor" href="#dreamlet-112"></a></h2>
 <ul><li>Nov 13, 2023</li>
 <li>
-<code><a href="../reference/computeLogCPM.html">computeLogCPM()</a></code> uses <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/augmentPriorCount.html" class="external-link">augmentPriorCount()</a></code>
+<code><a href="../reference/computeLogCPM.html">computeLogCPM()</a></code> uses <code>augmentPriorCount()</code>
 </li>
 </ul></div>
     <div class="section level2">
@@ -454,7 +459,7 @@ <h2 class="pkg-version" data-toc-text="0.0.51" id="dreamlet-0051">dreamlet 0.0.5
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.50" id="dreamlet-0050">dreamlet 0.0.50<a class="anchor" aria-label="anchor" href="#dreamlet-0050"></a></h2>
 <ul><li>Nov 2, 2022</li>
-<li>fix bug in <code><a href="http://gabrielhoffman.github.io/zenith/reference/zenith_gsa-methods.html" class="external-link">zenith_gsa()</a></code> for few gene sets</li>
+<li>fix bug in <code>zenith_gsa()</code> for few gene sets</li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.49" id="dreamlet-0049">dreamlet 0.0.49<a class="anchor" aria-label="anchor" href="#dreamlet-0049"></a></h2>
@@ -469,7 +474,7 @@ <h2 class="pkg-version" data-toc-text="0.0.48" id="dreamlet-0048">dreamlet 0.0.4
 </li>
 <li>and <code>alpha</code> arugment to <code><a href="../reference/plotVoom-methods.html">plotVoom()</a></code>
 </li>
-<li>update y axis and outlines in <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/plotVarPart-method.html" class="external-link">plotVarPart()</a></code>
+<li>update y axis and outlines in <code>plotVarPart()</code>
 </li>
 </ul></div>
     <div class="section level2">
@@ -478,7 +483,7 @@ <h2 class="pkg-version" data-toc-text="0.0.47" id="dreamlet-0047">dreamlet 0.0.4
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.46" id="dreamlet-0046">dreamlet 0.0.46<a class="anchor" aria-label="anchor" href="#dreamlet-0046"></a></h2>
-<ul><li>add <code>totalCPM</code> column to output of <code><a href="../reference/cellTypeSpecificity.html">cellTypeSpecificity()</a></code> to use for filtering. Functions <code><a href="../reference/plotHeatmap-methods.html">dreamlet::plotHeatmap()</a></code> <code><a href="../reference/plotViolin-methods.html">plotViolin()</a></code> and <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/plotPercentBars-method.html" class="external-link">plotPercentBars()</a></code> now ignore this column</li>
+<ul><li>add <code>totalCPM</code> column to output of <code><a href="../reference/cellTypeSpecificity.html">cellTypeSpecificity()</a></code> to use for filtering. Functions <code><a href="../reference/plotHeatmap-methods.html">dreamlet::plotHeatmap()</a></code> <code><a href="../reference/plotViolin-methods.html">plotViolin()</a></code> and <code>plotPercentBars()</code> now ignore this column</li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.45" id="dreamlet-0045">dreamlet 0.0.45<a class="anchor" aria-label="anchor" href="#dreamlet-0045"></a></h2>
@@ -488,7 +493,7 @@ <h2 class="pkg-version" data-toc-text="0.0.45" id="dreamlet-0045">dreamlet 0.0.4
 <h2 class="pkg-version" data-toc-text="0.0.44" id="dreamlet-0044">dreamlet 0.0.44<a class="anchor" aria-label="anchor" href="#dreamlet-0044"></a></h2>
 <ul><li>add <code><a href="../reference/plotGeneHeatmap-methods.html">plotGeneHeatmap()</a></code>
 </li>
-<li>add argument <code>assays</code> to <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/plotVarPart-method.html" class="external-link">plotVarPart()</a></code>
+<li>add argument <code>assays</code> to <code>plotVarPart()</code>
 </li>
 <li>add <code><a href="../reference/extractData-methods.html">extractData()</a></code>
 </li>
@@ -519,7 +524,7 @@ <h2 class="pkg-version" data-toc-text="0.0.39" id="dreamlet-0039">dreamlet 0.0.3
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.38" id="dreamlet-0038">dreamlet 0.0.38<a class="anchor" aria-label="anchor" href="#dreamlet-0038"></a></h2>
-<ul><li>add <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/getTreat-method.html" class="external-link">getTreat()</a></code> for <code><a href="../reference/dreamlet.html">dreamlet()</a></code> result</li>
+<ul><li>add <code>getTreat()</code> for <code><a href="../reference/dreamlet.html">dreamlet()</a></code> result</li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.37" id="dreamlet-0037">dreamlet 0.0.37<a class="anchor" aria-label="anchor" href="#dreamlet-0037"></a></h2>
@@ -577,14 +582,14 @@ <h2 class="pkg-version" data-toc-text="0.0.27" id="dreamlet-0027">dreamlet 0.0.2
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.26" id="dreamlet-0026">dreamlet 0.0.26<a class="anchor" aria-label="anchor" href="#dreamlet-0026"></a></h2>
 <ul><li>update <code><a href="../reference/dreamletCompareClusters.html">dreamletCompareClusters()</a></code>:
-<ul><li>now compatable with <code><a href="http://gabrielhoffman.github.io/zenith/reference/plotZenithResults.html" class="external-link">plotZenithResults()</a></code>
+<ul><li>now compatable with <code>plotZenithResults()</code>
 </li>
 <li>include flag <code>errorsAsWarnings</code>. If <code>TRUE</code> warns and returns NULL.</li>
 </ul></li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.25" id="dreamlet-0025">dreamlet 0.0.25<a class="anchor" aria-label="anchor" href="#dreamlet-0025"></a></h2>
-<ul><li>change return value for <code><a href="../reference/dreamletCompareClusters.html">dreamletCompareClusters()</a></code> to be compatible with <code><a href="http://gabrielhoffman.github.io/zenith/reference/zenith_gsa-methods.html" class="external-link">zenith_gsa()</a></code>
+<ul><li>change return value for <code><a href="../reference/dreamletCompareClusters.html">dreamletCompareClusters()</a></code> to be compatible with <code>zenith_gsa()</code>
 </li>
 <li>fix usage of <code>formula</code> in <code><a href="../reference/dreamletCompareClusters.html">dreamletCompareClusters()</a></code>
 </li>
@@ -633,10 +638,10 @@ <h2 class="pkg-version" data-toc-text="0.0.18" id="dreamlet-0018">dreamlet 0.0.1
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.17" id="dreamlet-0017">dreamlet 0.0.17<a class="anchor" aria-label="anchor" href="#dreamlet-0017"></a></h2>
 <ul><li>add <code><a href="../reference/run_mash.html">run_mash()</a></code>
-<ul><li>add <code><a href="http://gabrielhoffman.github.io/zenith/reference/zenith_gsa-methods.html" class="external-link">zenith_gsa()</a></code>, <code><a href="../reference/plotVolcano-methods.html">plotVolcano()</a></code>, <code><a href="../reference/plotForest-methods.html">plotForest()</a></code> for results</li>
+<ul><li>add <code>zenith_gsa()</code>, <code><a href="../reference/plotVolcano-methods.html">plotVolcano()</a></code>, <code><a href="../reference/plotForest-methods.html">plotForest()</a></code> for results</li>
 </ul></li>
 <li>fix bug in <code><a href="../reference/cellTypeSpecificity.html">cellTypeSpecificity()</a></code> for genes with zero reads across all cell types</li>
-<li>order of arguments in <code><a href="../reference/plotForest-methods.html">plotForest()</a></code> and <code><a href="http://gabrielhoffman.github.io/zenith/reference/zenith_gsa-methods.html" class="external-link">zenith_gsa()</a></code> changed for consistancy</li>
+<li>order of arguments in <code><a href="../reference/plotForest-methods.html">plotForest()</a></code> and <code>zenith_gsa()</code> changed for consistancy</li>
 <li>expand vignettes</li>
 <li>bug fix for <code><a href="../reference/removeConstantTerms.html">removeConstantTerms()</a></code> when excluded variable string (i.e. tissue) is also a substring of other variables (i.e. tissueStatus)</li>
 </ul></div>
@@ -646,7 +651,7 @@ <h2 class="pkg-version" data-toc-text="0.0.16" id="dreamlet-0016">dreamlet 0.0.1
 <li>add <code>dreamletPairs()</code>
 </li>
 <li>fix bug in <code><a href="../reference/removeConstantTerms.html">removeConstantTerms()</a></code> with multiple constant terms</li>
-<li>improve usability of <code><a href="../reference/cellTypeSpecificity.html">cellTypeSpecificity()</a></code> by adding <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/plotPercentBars-method.html" class="external-link">plotPercentBars()</a></code> and <code><a href="../reference/plotViolin-methods.html">plotViolin()</a></code> compatability</li>
+<li>improve usability of <code><a href="../reference/cellTypeSpecificity.html">cellTypeSpecificity()</a></code> by adding <code>plotPercentBars()</code> and <code><a href="../reference/plotViolin-methods.html">plotViolin()</a></code> compatability</li>
 <li>fix bug in <code>topTable()</code> when <code>coef</code> is not estimated</li>
 <li>add argument <code>assays</code> to <code><a href="../reference/dreamlet.html">dreamlet()</a></code>, <code><a href="../reference/fitVarPart.html">fitVarPart()</a></code>, and <code><a href="../reference/processAssays.html">processAssays()</a></code>
 </li>
@@ -655,11 +660,11 @@ <h2 class="pkg-version" data-toc-text="0.0.16" id="dreamlet-0016">dreamlet 0.0.1
 <h2 class="pkg-version" data-toc-text="0.0.15" id="dreamlet-0015">dreamlet 0.0.15<a class="anchor" aria-label="anchor" href="#dreamlet-0015"></a></h2>
 <ul><li>
 <code><a href="../reference/processOneAssay.html">processOneAssay()</a></code> weights by number of cells</li>
-<li>require <code>variancePartition &gt;= 1.25.1</code> to handle weights in <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/voomWithDreamWeights.html" class="external-link">voomWithDreamWeights()</a></code>
+<li>require <code>variancePartition &gt;= 1.25.1</code> to handle weights in <code>voomWithDreamWeights()</code>
 </li>
 <li>fix bug in <code>topTable()</code>
 </li>
-<li>add <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/plotPercentBars-method.html" class="external-link">plotPercentBars()</a></code> for class <code>vpDF</code>
+<li>add <code>plotPercentBars()</code> for class <code>vpDF</code>
 </li>
 <li>misc bug fixes</li>
 <li>improve documentation</li>
@@ -667,7 +672,7 @@ <h2 class="pkg-version" data-toc-text="0.0.15" id="dreamlet-0015">dreamlet 0.0.1
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.0.14" id="dreamlet-0014">dreamlet 0.0.14<a class="anchor" aria-label="anchor" href="#dreamlet-0014"></a></h2>
 <ul><li>move count ratio code to crumblr package</li>
-<li>use <code><a href="http://DiseaseNeurogenomics.github.io/variancePartition/reference/applyQualityWeights.html" class="external-link">applyQualityWeights()</a></code>
+<li>use <code>applyQualityWeights()</code>
 </li>
 </ul></div>
     <div class="section level2">
@@ -699,7 +704,7 @@ <h2 class="pkg-version" data-toc-text="0.0.10" id="dreamlet-0010">dreamlet 0.0.1
 <li><p>suppress package startup messages in <code><a href="../reference/aggregateToPseudoBulk.html">aggregateToPseudoBulk()</a></code></p></li>
 <li><p>bug fix in <code><a href="../reference/removeConstantTerms.html">removeConstantTerms()</a></code></p></li>
 <li><p>Sept 30, 2021</p></li>
-<li><p>call to <code><a href="http://gabrielhoffman.github.io/zenith/reference/zenith_gsa-methods.html" class="external-link">zenith_gsa()</a></code> adds argument <code>inter.gene.cor</code> and <code>progressbar</code></p></li>
+<li><p>call to <code>zenith_gsa()</code> adds argument <code>inter.gene.cor</code> and <code>progressbar</code></p></li>
 <li><p>fix output to <code>cellTypeCompositionVarPart()</code> and <code>cellTypeCompositionTest()</code></p></li>
 <li><p>fix issue with <code>topTable()</code> where FDR was evaluated on only a subset of genes</p></li>
 </ul></div>