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Overview

  • Description
  • Key Features

Getting Started

  • Installation guide
    • Using a virtual environment
    • Installing with pip
    • Installing from github
    • Dependencies
      • Required Dependencies
      • Optional dependencies
  • Quick demo
  • Workflow

API Description

  • Classes
    • CreateVariants class
    • Counts class
      • LibraryRepresentation pyplot class
      • MeanCounts pyplot class
    • GeneratePrimers class
    • Screen class
      • EnrichmentBar pyplot class
      • Differential pyplot class
      • PositionBar pyplot class
      • Secondary pyplot class
      • Kernel pyplot class
      • Histogram pyplot class
      • Sequence pyplot class
      • MultipleKernel pyplot class
      • Heatmap pyplot class
      • HeatmapColumns pyplot class
      • HeatmapRows pyplot class
      • Miniheatmap pyplot class
      • Rank pyplot class
      • Cumulative pyplot class
      • ROC pyplot class
      • Correlation pyplot class
      • IndividualCorrelation pyplot class
      • PCA pyplot class
      • DifferentialP plotly class
      • EnrichmentBarP plotly class
      • HeatmapP plotly class
      • HistogramP plotly class
      • RankP plotly class
      • Scatter3DPDB plotly class
      • Scatter3D plotly class
      • ScatterP plotly class
      • Scatter pyplot class
      • ScatterReplicates pyplot class
      • Pymol pyplot class
  • Functions

Tutorial

  • Tutorial introduction
  • Design DNA libraries
    • Design primers
    • Design site-saturation sequences
  • Processing DNA reads
    • Import module
    • Count DNA reads from fastq file
      • Site saturation mutagenesis
      • Custom DNA list
    • Calculate enrichment scores
  • Normalizing datasets
    • Import modules and load data
    • Calculate log10 enrichment
    • Centering the data (zeroing)
      • Counts normalization
      • Wt allele
      • Distribution of synonymous wt alleles
      • Wt alleles observation
      • Distribution of mutants
    • Baseline subtraction
    • Scaling
    • Multiple sublibraries
    • Heatmaps
  • Creating heatmaps
    • Import modules
    • Create object of class Screen
    • Heatmaps
    • Heatmap slices
    • Miniheamap
    • Reference
  • Creating plots
    • Import modules
    • Histogram, scatter and more
    • Bar and line charts
    • Correlation, PCA and ROC AUC
    • Pymol
    • Art
    • Reference
  • Visualizing with plotly
    • Heatmap
    • Mean
    • Histogram
    • Rank
    • Scatter
    • 3D scatter plot
    • PDB properties
  • Other datasets
    • Load objects
    • Hidalgo et al. eLife 2022 paper
    • Beta Lactamase
      • Create object
      • 2D Plots
      • 3D Plots
    • Sumo1
      • Create object
      • 2D Plots
    • MAPK1
      • Create object
      • 2D Plots
    • UBE2I
      • Create object
      • 2D Plots
    • TAT
      • Create object
      • 2D Plots
    • REV
      • Create object
      • 2D Plots
    • α-synuclein
      • Load data
      • 2D Plots
    • APH(3) II
      • Create object
      • 2D Plots
      • 3D plots
    • b11l5f
      • Create object
      • 2D Plots
    • References

About Us

  • Bio
    • Frank Hidalgo
    • Sage Templeton
    • Che Olavarria Gallegos
    • Joanne Wang
mutagenesis_visualization
  • Docs »
  • Search
  • Edit on GitHub

© Copyright 2021, Frank Hidalgo Revision f2db9049.

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