Preview

Arcadia-Science-toxin-facilitators-052b43b
- .gitignore
  
  94 Bytes
- LICENSE
  
  1.1 kB
- README.md
  
  31.2 kB
- environment.yml
  
  253 Bytes
- figures
  - Fig3.html
    
    4.0 MB
  - Fig4_outliers_toxin_heatmap_interactive.html
    
    5.6 MB
  - Fig5.pdf
    
    7.2 kB
  - Fig6.pdf
    
    6.1 kB
  - Outlier_visualization.pdf
    
    1.8 MB
- metadata
  - Matrix_Outliers.tsv
    
    19.0 kB
  - R_scripts_data
    - Cluster_Acc_Ref_PFAM_UpdatedJune2023.csv
      
      20.5 kB
    - Origin_data_accessory_seq_clusters_UpdatedJune2023.csv
      
      522.8 kB
    - Outliers_data_Figure1B.csv
      
      114.2 kB
    - Uniprot_Cluster_Info.csv
      
      52.8 kB
  - SRA_TSA_venom_gland_accessions.csv
    
    29.1 kB
  - SRA_TSA_venom_gland_accessions_fastarna_list.csv
    
    2.8 kB
  - SRA_TSA_venom_gland_accessions_protein_list.csv
    
    1.6 kB
  - ixodida_genomes.txt
    
    1.6 kB
  - toxin_list.txt
    
    3.8 kB
  - toxin_pfam_accessions.txt
    
    5.2 kB
- notebooks
  - Figure4_Interactive_toxin_outlier_heatmap.ipynb
    
    10.8 kB
  - toxin_clusters_summary_report.Rmd
    
    12.5 kB
  - toxin_clusters_summary_report.html
    
    2.3 MB
  - toxin_facilitator_report.Rmd
    
    3.1 kB
  - toxin_facilitator_report.html
    
    1.0 MB
  - toxin_facilitator_report.log
    
    35 Bytes
  - toxin_facilitator_report.tex
    
    15.9 kB
- results
  - 2023-04-05_v1
    - all_additional_pfam_annotations.txt
      
      24.9 kB
    - all_pfam_hits.out
      
      1.4 MB
    - hits.txt
      
      2.1 MB
    - summary.txt
      
      499.8 kB
    - toxin-additional-domain-annotations-hits.csv
      
      32.9 kB
  - 2023-04-13-clustering-results
    - uniprot-vs-venom-proteins-summaries.tsv
      
      8.0 MB
  - 2023-04-26-clustering-results
    - uniprot-toxin-proteins-outliers.xlsx
      
      26.8 kB
    - uniprot-vs-all-venom-tick-proteins-results.tsv
      
      5.1 MB
    - uniprot-vs-all-venom-tick-proteins-summaries.tsv
      
      9.2 MB
  - 2023-05-01-diamond-uniprot
    - lists
      - outlier-protein-hits-list.txt
        
        35.0 kB
    - results
      - accessory-toxin-proteins-clustering_cluster.tsv
        
        230.4 kB
      - hits.txt
        
        378.4 kB
      - summary.txt
        
        20.4 kB
      - uniprot-toxins-outliers-ranges.txt
        
        434.4 kB
      - uniprot-toxins-rep-seqs-vs-outlier-hit-proteins.txt
        
        201.5 kB
      - uniprot-toxins-vs-outlier-hit-proteins.txt
        
        923.5 kB
  - 2023-06-01-updated-clustering-results
    - results
      - uniprot-vs-venom-proteins-results.tsv
        
        7.6 MB
      - updated-uniprot-vs-venom-proteins-summaries.tsv
        
        14.7 MB
  - 2023-06-15-exhaustive-clustering-results
    - results
      - 2023-06-15-updated-uniprot-vs-venom-tick-proteins-results.tsv
        
        9.5 MB
      - 2023-06-15-updated-uniprot-vs-venom-tick-proteins-summaries.tsv
        
        18.9 MB
  - 2023-06-20-diamond-uniprot
    - lists
      - 2023-06-20-updated-outliers-list.txt
        
        35.0 kB
      - Venomproteins_ticks_toxins_outliers_new.csv
        
        45.3 kB
    - results
      - 2023-06-20-outliers-ranges.txt
        
        340.6 kB
      - 2023-06-20-uniprot-toxins-vs-updated-outliers-hits.txt
        
        857.7 kB
      - updated-accessory-toxin-cluster-pfam-hmmer-output.txt
        
        410.0 kB
      - updated-accessory-toxin-cluster-pfam-hmmer-summary.txt
        
        19.1 kB
      - updated-accessory-toxin-clustering_cluster.tsv
        
        174.2 kB
  - Results_R_Analysis
    - ASClusters_metrics_summary_UpdatedJune2023.csv
      
      4.0 kB
    - Accessory_clusters_nonToxin_UpdatedJune2023.csv
      
      21.5 kB
    - Clusters_Accessory_UpdatedJune2023.csv
      
      176.8 kB
    - Data_summary_acc_cluster_no1_UpdatedJune2023.csv
      
      3.5 kB
    - Venomproteins_ticks_toxins_outliers_June2023.csv
      
      246.7 kB
  - Tables
    - Table-1_Accessory_clusters_non_Toxin_Pfam_information.xlsx
      
      12.6 kB
    - Table-2_Summary_metrics_accessory_sequence_clusters_.csv
      
      3.5 kB
- scripts
  - Accessory_sequence_diversity_analysis.R
    
    7.6 kB
  - Length-outliers-search.R
    
    7.7 kB
  - download_venom_fasta_accessions.py
    
    3.4 kB
  - download_venom_tsa_proteins.py
    
    3.3 kB
  - make_subset_fasta.py
    
    927 Bytes
  - parse_mmseqs_results.py
    
    3.0 kB
  - remove-blast-hit-from-protein.py
    
    2.6 kB
  - reorganize_fastas.py
    
    1.3 kB
  - run_all_pfam.py
    
    2.9 kB
  - run_parse_hmms.py
    
    3.5 kB
  - run_transdecoder.sh
    
    449 Bytes
- toxin_facilitators.Rproj
  
  205 Bytes

Arcadia-Science/toxin-facilitators-v1.0pub.zip