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index.Rmd
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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)
* [Look at number of reads lost if you exclude reads with N](index.html)
* [Base composition](BaseComp.html)
* [Change misprimming parameters](changeMisprimcut.html)
* [Test for annotation bias](annotationBias.html)
### Choosing cuttoffs for usage and expression level
* [Use merged 3' at gene level to look for a data quantity cutoff](expressioncutoff.html)
* [Establish cutoffs by subsampleing apaQTL lines](establishCutoffs.html)
* [Compare before and after cutoff](compareFilter.html)
##Catalog PAS:
* [Number of PAS in each species](PASnumperSpecies.html)
* [Number of PAS in each species double filter](PASnumberSpecies_doubleFilter.html)
* [Pressence of top 2 signal sites](signalsites.html)
* [Top 2 signal sites double filter](signalsites_doublefilter.html)
* [Dominant PAS in Nuclear Fraction](dominantPAS.html)
* [Dominant PAS in Nuclear Fraction double filter](dominantPAS_DF.html)
* [Intronic location for dominant PAS](DominantPASintronLoc.html)
* [Intronic location for dominant PAS double filter](DominantPASintronLoc_DF.html)
* [Species Specificity in PAS](speciesSpecific.html)
* [Species Specificity in PAS double filter](speciesSpecific_DF.html)
##Differential Isoform Analysis:
* [Nuclear Human vs. Chimp Analysis](Nuclear_HvC.html)
* [Nuclear Human vs. Chimp Analysis Double filter](Nuclear_HvC_DF.html)
* [Explore nuclear differential APA PAS and genes](Explore.html)
* [Explore nuclear differential APA PAS and genes Double filter](Explore_DF.html)
* [Enrichment for differencial APA and apaQTL](andapaQTL.html)
* [Enrichment for differencial APA and apaQTL double filter](dAPAandapaQTL_DF.html)
* [Visualization for all Nuclear DAPA genes](visualizePASUsage.html)
* [Visualization for all Nuclear DAPA genes double filter](visualizePASUsage_DF.html)
From here on, I did everything double filtered:
* [Does presence or absense of signal explain differential usage](SS_diffUsage.html)
* [Protein interactions](PTM_analysis.html)
##Human v Chimp fraction differences
* [Differential isoform between fractons by species](TotalVNuclearBothSpecies.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)
* [Compare to nuclear differential APA with Double filter](DiffTransProtvsNuclearAPA_DF.html)
* [Use UpSetR to vizualize intersections](upsetter.html)
* [Use UpSetR to vizualize intersections Double filter](upsetter_DF.html)
* [Effect size correlations](correlationPhenos.html)
* [Effect size correlations double filter](correlationPhenos_DF.html)
All with double filter:
* [Compare species 5' splice site strength](SpliceSiteStrength.html)
##Selection exploration
* [Explore PAS conservation](dAPA_Conservation.html)
* [Use directional selection from Khan](DirSelectionKhan.html)
##Mediation
* [Normalize Nuclear Fraction](NormalizePheno_nuclear.html)
* [Normalize (qqnrom) Nuclear Fraction double filter](NormalizePheno_nuclear_DF.html)
* [Normalize clusters from splicing analysis](normalizeClusters.html)
* [Mediation analysis](mediation.html)
* [Mediation analysis double filter](mediation_DF.html)
From here on, I did everything double filtered:
* [Mediation with protein](mediation_prot.html)
* [Explore more about APA expression relationship](ExploreAPAexpression.html)
* [Explore more about APA expression relationship with overlaping significant genes](ExploreAPAexpressionOverlap.html)
* [Apa and expression relationship for seperated by location of PAS](DiffUsedIntronic.html)
* [Look at genes that have differences in protein levels and APA levels but not mRNA expression](dAPAdPnotE.html)
###Visualization
* [Try to use gviz](GvizPlots.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)
### 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)
### Extra comparisons or analysis: not redone after double filter
* [Human Total vs Nuclear Analysis](Human_TvN.html)
* [Chimp Total vs Nuclear Analysis](Chimp_TvN.html)
* [Dominant PAS in Total Fraction](dominantPAS_total.html)
* [Total Human vs. Chimp Analysis](Total_HvC.html)
* [Venn diagrams for genes in each differential APA set](CompHC_totalandnuclear.html)
From the original nuclear dominant
* [Does signal site explain trend?](ss_sameDomdiffDom.html)
* [Look at Intronic Dominant with DPAU and DE](HumanIntronicDominant.html)
* [Enrichment for differencial APA and eQTL](DapaineQTL.html)
* [Look at dAPA and genes from Dominant PAS analysis](DominatPASandDIffAPA.html)