update website

docs/heatmaps.md

@@ -41,13 +41,15 @@ If protein structure is available, distance in angstroms to the closest antibody
 ::: tip
 Click arrow in upper right to view full-sized plots
 :::
-Effects of mutations on cell entry and binding at receptor contact sites
+Effects of mutations on cell entry and binding at receptor contact sites. Receptor contact sites are less constrained for entry in CHO-bEFNB2 cells than CHO-bEFNB3 cells, likely due to ~25-fold higher receptor affinity.
 <Altair :showShadow="true" :spec-url="'htmls/combined_entry_binding_contact_heatmaps.html'"></Altair>
 
 ### Effects of mutations on cell entry and binding at glycosylation sites
+Nipah RBP has six sites that are glycosylated. One in the neck (site 159) and five in the head. Here are the effects of mutations on entry and binding.
 <Altair :showShadow="false" :spec-url="'htmls/glycan_sites_img_heatmap.html'"></Altair>
 
 ### Effects of mutations on cell entry and binding at polymorphic Nipah sites
+These sites are polymorphic in Nipah sequences. Most of these sites tolerate multiple mutations. 
 <Altair :showShadow="true" :spec-url="'htmls/nipah_poly_sites_img_heatmap.html'"></Altair>
 
 ### Effects of mutations on cell entry, organized by type of the unmutated amino acid residue 

docs/pipeline_information.md

@@ -13,7 +13,7 @@ max_minor_indel_frac=0.2
 min_support=3
 ```
 
-These parameters filter consensus sequences generated from Pacbio CCS sequencing and assembly. If a consensus RBP sequence has a mutation or indel in more than 20% of the reads, it will be discarded. Consensus sequences must have at least three reads to be included as variants.
+These parameters filter consensus sequences generated from Pacbio CCS sequencing and assembly. If an assembled RBP sequence has a mutation or indel in more than 20% of the reads, it will be discarded. Consensus sequences must have at least three reads to be included as variants.
 
 
 ## Analyze PacBio CCS Reads
@@ -26,13 +26,13 @@ Reports information about CCS read filtering.
 
 <a href="notebooks/build_codon_variants.html" target="_self">Build codon variants notebook</a>
 
-Builds the codon-variant table from PacBio consensus sequences that links barcodes and mutations. 
+Builds the codon-variant table from PacBio consensus sequences that links barcodes and RBP mutations. 
 
 [Link to codon-variant table .csv file](https://github.com/dms-vep/Nipah_Malaysia_RBP_DMS/blob/master/results/variants/codon_variants.csv){target="_self"}
 
 
 ## Illumina Variant Counts
-Once the barcodes are linked to mutations in the codon-variant table, all sequencing data is generated with Illumina to obtain the relative frequencies of barcodes in each selection experiment.  
+Once the barcodes are linked to mutations in the codon-variant table, all sequencing data is generated with Illumina on a small sequence fragment to obtain the relative frequencies of barcodes in each selection experiment.  
 
 <a href="notebooks/analyze_variant_counts.html" target="_self">Analysis of variant counts notebook</a>
 
@@ -42,7 +42,7 @@ Once the barcodes are linked to mutations in the codon-variant table, all sequen
 
 <a href="notebooks/filter_data.html" target="_self">Filtering notebook</a>
 
-The final averaged data were filtered based on the following parameters that are contained within the [nipah_config.yaml](https://github.com/dms-vep/Nipah_Malaysia_RBP_DMS/blob/master/nipah_config.yaml){target="_self"} file. More information about these parameters are listed in the notebook.
+The final averaged data were filtered based on parameters that are contained within the [nipah_config.yaml](https://github.com/dms-vep/Nipah_Malaysia_RBP_DMS/blob/master/nipah_config.yaml){target="_self"} file. More information about these parameters are listed in the notebook.
 
 ## Raw Filtered Data
 ::: tip These data have been filtered. For pre-filtered raw .csv files, go to individual pages to view and download.

docs/receptor_binding.md

@@ -1,6 +1,6 @@
 # Receptor Binding
 
-To understand how mutations affect binding to soluble receptor, we performed selections on our pseudovirus libraries with soluble receptor. Neutralization of pseudovirus variants serves as a proxy for receptor binding. Receptor binding selections were fit with [polyclonal](https://github.com/jbloomlab/polyclonal){target="_self"}.
+To understand how mutations affect binding to soluble receptor, we performed selections on our pseudovirus libraries with soluble receptor. Neutralization of pseudovirus variants serves as a proxy for receptor binding. Neutralization curves were fit with [polyclonal](https://github.com/jbloomlab/polyclonal){target="_self"}.
 
 
 ## Individual Receptor Binding Selections
@@ -21,11 +21,10 @@ To understand how mutations affect binding to soluble receptor, we performed sel
 
 <a href="notebooks/fit_escape_receptor_affinity_LibB-230907-bEFNB3-dimeric.html" target="_self">LibB-230907-bEFNB3-dimeric</a>
 
-<a href="notebooks/fit_escape_receptor_affinity_LibB-231108-EFNB3-monomeric.html" target="_self">LibB-231108-EFNB3-monomeric</a>
 :::
 
 ## Average Receptor Binding
-Averaging receptor binding across libraries and replicate selections.
+These notebooks average effects of mutations on receptor binding across libraries and replicate selections.
 
 <a href="notebooks/avg_escape_receptor_affinity_bEFNB2_monomeric.html" target="_self">bEFNB2_monomeric</a>