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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
---
Welcome to my research website.
##Preprocessing:
In the preprocessing steps of the analysis I will go from the fastq files that come off the sequencer to the PAS I will use for the rest of the analysis.
* [Process fastq to cleaned bam files](fastq2bam.html)
* [Process bam to PAS](bam2pas.html)
##QC and base visualization:
These files create some of the QC metrics I used for the analysis.
* [Look at PAS usage differences by gene coverage](PASusageQC.html)
* [Look at read distribution accross features](Readdistagainstfeatures.html)
* [Make descriptive plots for called PAS](PASdescriptiveplots.html)
* [Plot signal site dristributions](signalsiteanalysis.html)
* [Count and usage correlation](corrbetweenind.html)
* [Sequencing meta data by batch](seqmetadatanalysis.html)
* [Understand new PAS](NewvOldPeakQC.html)
* [Compare new and old data](recomputeusageold.html)
* [Look at coverage in 3' UTR](reads2UTR.html)
* [Intron RNA seq ratios](intonRNAratio.html)
* [Prepare genotypes for downstream analysis](geno_proc.html)
* [Compare to Annotations](compareAnnotatedpas.html)
* [Addition coverage plots](additionalCoveragePlots.html)
##apaQTL
* [Call apaQTLs in both fractions](mapapaQTL.html)
* [Check for batch effects in new QTLs](newQTLheatmap.html)
* [Look at how many PCs I should include](choosePCs.html)
* [Code to make example plots](QTLexampleplots.html)
* [Rerun qtl with PCs from previous analysis](rerunQTL_changePC.html)
* [Location of QTLs with respect to PAS and gene body](QTLlocation.html)
* [apaQTL in opposite fraction](apaQTLoverlap.html)
* [Usage QTL analysis to look at non normal effect sizes](nonNormQTL.html)
* [Motif distruption as apaQTL mechanism](motifDisruption.html)
* [Are snps in Signal sites likely to be QTLs?](snpinSS.html)
* [Transcription factor motif disruption for QTLs](TF_motifdisrupt.html)
* [Gene Ontology](GO_apaQTLS.html)
* [2 Regulatory mechanisms for apaQTLs](twoRegMech.html)
* [Pre-termination QTLs](PrematureTermQTL.html)
* [Overlap pttQTL and apaQTLs](pttgeneinAPA.html)
##Differential Isoform Analysis
* [Run leafcutter to compare fractions](DiffIsoAnalysis.html)
* [Results when logef > 0.5](diffiso_logef5.html)
* [Results when logef > 1](diffuse_logef1.html)
* [Regulatory correlation heatmap](rna_netseq_h3k12ac.html)
* [Relationship between APA fraction and nascent transcription](nascenttranscription.html)
* [Location of nuclear intronic peaks along introns](nucintronicanalysis.html)
* [Explore first intron PAS further](verifyFirstintronresult.html)
* [Start looking at the nascent seq](nascentRNA.html)
* [Credible set with RNA and signal sites](HighCrediblePAS.html)
##Characterize apaQTLs and compare to eQTLs
* [Analysis to look at differences in QTL chromHMM categories](chromHHMQTL.html)
* [Comparing explained and unexplained eGenes](exvunexpeQTL.html)
* [Proportion explained](propeQTLs_explained.html)
* [Nuclear specific apaQTLs](NuclearSpecAPAqtl.html)
* [Nuclear specific apaQTLs and differential usage](usageNucspecapaQTLs.html)
* [New way to look at nuclear specific, include not tested in total](NuclearSpecIncludeNotTested.html)
* [Comparing protein specific genes with apaQTL](pQTLandeQTLoverlap.html)
* [Rerun eQTLs and pQTLs for use in overlap analysis](molQTL.html)
* [eQTL and pQTL effect sizes for apaQTLs](eQTLeffectNucspecapa.html)
* [Nuclear specific apaQTL genes in eQTL results](nucSpecinEQTLs.html)
* [pQTL example](pQTLexampleplot.html)
* [pttQTL in expression data](pttQTLinE.html)
* [GWAS overlap](gwasOverlap.html)
##Graph from Mayher
* [Location and usage of PAS](PAS_graphs.html)
* [Read metadata plots](reads_graphs.html)