index.Rmd

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title: "Home"
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Website to share results of fucci-seq project.

## Overview

* [Data description](data-overview.html)

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## Microscopy image analysis

* [Processing images - from images to intensities](images-process.html)

* Image inspection
    * [Inspect images with multiple nuclei](images-multiple-nuclei.html)
    * [Inspect images with no nucleus](images-zero-nuclei.html)

* Image intensities
    * [CONFESS results](confess-prelim.html)
    * [QC analysis including no. nuclei detected, DAPI, and intensity variation](images-qc.html)
    * [Explore using log10 sum pixel intensity for signal metrics](images-qc-followup.html)
    * [Compare correction approaches using median versus mean background](images-metrics.html)
    
* Shape metrics
    * [Nucleus shape metrics versus intensities](images-metrics-cell-shape.html)

* Normalize intensities by batch
    * [Visualize signal variation by plate and individual identity](images-qc-labels.html)
    * [Visualize the structure of signal variation by individual identity](images-qc-variation.html)
    * [Quantile normalization for GFP, RFP and DAPI](images-normalize-quantile.html)
    
* transgene count in sequencing data
    * [Investigate zero-count transgenes](images-transgene.html)

* Cluster cells based on FUCCI
    * [Partition around medoids(PAM)](images-pam.html)
    * [Mixture modeling](images-mclust.html)
    * [Select a subset using silhouette index](images-subset-silhouette.html)

* Fitting cellcycleR
    * [Parametric model across plates and individuals](images-cellcycleR.html)
    * [Model convergence assessment](images-cellcycleR-convergence.html)
    

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## Qualty Control

* Sample QC and filtering
    * [Sample QC criteria](sampleqc.html)  
    * [Sequencing depth](totals.html)  
    * [Reads versus molecules](reads-v-molecules.html)  

* Gene QC and filtering
    * [gene filtering](gene-filtering.html)
    * [PCA with technical fators](pca-tf.html)