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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
I am interesting in understanding differential APA between human and chimpanzees. I used 3' Seq to identify PAS for total and nuclear frations of LCL in both species.
##Preparation and QC:
* [Prepare annotation files for mapping ](annotationInfo.html)
* [Mapping statistics and plots](mapStats.html)
* [Liftover PAS](liftoverPAS.html)
* [Annotated PAS and make APA phenotype](annotatePAS.html)
* [Compare identified PAS with apaQTL PAS](comp2apaQTLPAS.html)
* [PCA plot to look at variation in data](NromalizePhenos.html)
* [Correlation between individuals](CorrbetweenInd.html)
* [Verify sample identity](verifyBAM.Rmd)
* [3' Seq enrichement along gene bodies](EnrichmentEndofGenes.html)
* [Cross map and prepare Chimp 3' for Viz in IGV](CrossChimpThreePrime.html)
* [Make PAS bed for 5% peaks](fixPeak2PAS.html)
##Catalog PAS:
* [Number of PAS in each species](PASnumperSpecies.html)
* [Pressence of top 2 signal sites](signalsites.html)
* [Dominant PAS in Total Fraction](dominantPAS_total.html)
* [Dominant PAS in Nuclear Fraction](dominantPAS.html)
* [Intronics location for dominant PAS](DominantPASintronLoc.html)
* [Does signal site explain trend?](ss_sameDomdiffDom.html)
##Differential Isoform Analysis:
* [Human Total vs Nuclear Analysis](Human_TvN.html)
* [Chimp Total vs Nuclear Analysis](Chimp_TvN.html)
* [Nuclear Human vs. Chimp Analysis](Nuclear_HvC.html)
* [Total Human vs. Chimp Analysis](Total_HvC.html)
* [Venn diagrams for genes in each differential APA set](CompHC_totalandnuclear.html)
* [Differential APA and eQTL overlap](DapaineQTL.html)
* [Look at dAPA and genes from Dominant PAS analysis](DominatPASandDIffAPA.html)
##Quantify Phenotypes with RNA:
* [Differential Splicing](diffSplicing.html)
* [Differential Expression](diffExpression.html)
* [Metadata by species](MetabySpecies.html)
* [DE genes and eQTLs](DEandeQTls.html)
* [Compare DE and DS genes](DEvDS.html)
##Intersect with outside molecular phenotypes:
* [Download data from differential protein and ribosomes](dProtanddRibo.html)
* [Compare to nuclear differential APA](DiffTransProtvsNuclearAPA.html)
* [Use UpSetR to vizualize intersections](upsetter.html)
##Extra QC and Analysis
### Sample switch analysis
* [Investigate bad RNA seq samples](InvestigateBadSamples.html)
* [Differential splicing without bad samples](diffSplicing_removeBad.html)
* [Differential Expression without bad samples](diffExpressionRemove2.html)
### Mapping problems with pantro5 and multimapping
* [Map RNA to hg19](MapRNAhg19.html)
* [Evaluate multimapping criteria](multiMap.html)
* [Map to opposite Genomes](OppositeMap.html)
* [Evaluate Pantro 5 problems](investigatePantro5.html)
From before reseq:
* [Total Fraction](NormalizePheno_total.html)
* [Total Fraction- Prenormalized](NonNormPheno_total.html)
* [Nuclear Fraction](NormalizePheno_nuclear.html)
### Chosing between pantro files
* [Compare pantro5 and pantro6 orthoexon](compareOrthoExon.html)
* [Differential Expression with Pantro6](diffExpressionPantro6.html)
* [Compare DE in pantro5 vs pantro6](DE_pantro5vspantro6.html)