update readmes, fix typo and path in website

README.md

@@ -1,9 +1,12 @@
 # Deep mutational scanning of the Nipah virus receptor binding protein (RBP) using a barcoded lentiviral vector
-Study by Brendan Larsen, Teagan McMahon and Jesse Bloom.
+Study by Brendan Larsen, Teagan McMahon, Jack T. Brown, Zhaoqiang Wang, Caelan E. Radford, James E Crowe Jr., David Veesler, and Jesse Bloom.
 
-For a landing page that contains additional information about the project, see [https://dms-vep.github.io/Nipah_Malaysia_RBP_DMS/](https://dms-vep.github.io/Nipah_Malaysia_RBP_DMS/).
+For a website that contains additional information about the project, including links to raw data and interactive data visualizations, see [https://dms-vep.github.io/Nipah_Malaysia_RBP_DMS/](https://dms-vep.github.io/Nipah_Malaysia_RBP_DMS/).
 
+## Links to raw data
+If you are interested in viewing or analyzing the final, filtered deep mutational scanning data, see [results/filtered_data/public_filtered/](results/filtered_data/public_filtered)
 
+## Information about project
 This repo contains data and analyses from deep mutational scanning experiments on the Nipah virus RBP. All experiments were performed on the reference Nipah genome sequenced during the original outbreak in Malaysia [NC_002728.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_002728.1). Thirty two amino acids were removed from the cytoplasmic tail to improve lentivirus titers, and all residues between RBP reference sites 71 and 602 contain every possible single missense mutation. Stop codons were designed to occur at every other position from positions 71 to 234.
 
 ## Details of repo

data/custom_analyses_data/README.md

@@ -5,34 +5,31 @@ This subdirectory contains input data used by custom analyses jupyter notebooks
 * File for setting custom altair themes, used by most notebooks for plotting
 
 [heatmap_theme.py](heatmap_theme.py): 
-* File for setting custom altair themes, used by scripts to make heatmaps
+* File for setting custom altair themes, used by notebooks to make heatmaps
 
 [interactive_theme.py](interactive_theme.py):
-* File for setting custom altair themes, used by scripts to make large interactive figures
+* File for setting custom altair themes, used by notebooks to make large interactive figures
 
-### Surface Exposure
-[surface_exposure.csv](surface_exposure.csv): 
-* This file contains information about the relative surface exposure of Nipah RBP residues
 
 ### Paper Supplementary Data
 [./paper_supplementary_data](paper_supplementary_data):
 * Supplemental data for paper
 
 ### Alignments and phylogenetics
-[./alignments](alignments): 
+[/alignments](alignments): 
 * **ephrin_E2_E3_sequences.fasta** Amino acid alignment of Human and Pteropus alecto EFNB2 and EFNB3
 * **Nipah_RBP_AA_align.fasta** Alignment of Nipah RBP sequences downloaded from GenBank
 * **wild_type_seq.fasta** wildtype sequence (non codon-optimized) of NiV-M RBP
 * **Nipah-B_MK673572.1.fasta** wildtype sequence of NiV-B RBP
 
-[./alignments/phylo](phylogenetics):
+[/alignments/phylo](phylogenetics):
 * **country_genbank_ids.csv** Country of origin of genbank sequences
 * **nipah_whole_genome_alignment.fasta** Alignment of whole genome nipah sequences
 * **nipah_whole_genome_genbank_accession_ids.txt** Accession IDs from genbank
 * **nipah_whole_genome_phylo.tre** Phylogeny of whole genome nipah sequences inferred from IQ-TREE
 
 ### Protein crystal structures
-[./crystal_structures](crystal_structures):
+[/crystal_structures](crystal_structures):
 **PDB files of:**
 * **2vsm.pdb** (Nipah RBP bound to Ephrin-B2)
 * **3d12.pdb** (Nipah RBP bound to Ephrin-B3)
@@ -42,6 +39,6 @@ This subdirectory contains input data used by custom analyses jupyter notebooks
 * **7txz.pdb** (Partial Nipah RBP bound to nAH1.3)
 
 ### Experimental data
-[./experimental_data](experimental_data): **Raw experimental data of relative light units (RLUs) or fraction infectivity neutralization experiments. Also includes mAb, binding, and cell entry validation data. More information in readme in directory**
+[/experimental_data](experimental_data): **Raw experimental data of relative light units (RLUs) or fraction infectivity neutralization experiments. Also includes mAb, binding, and cell entry validation data. More information in readme in directory**