-
Notifications
You must be signed in to change notification settings - Fork 1
/
index.Rmd
164 lines (80 loc) · 4.26 KB
/
index.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
---
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)
### 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)
##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)
- [Intronics location for dominant PAS](DominantPASintronLoc.html)
- [Does signal site explain trend?](ss_sameDomdiffDom.html)
- [Look at Intronic Dominant with DPAU and DE](HumanIntronicDominant.html)
* [Species Specificity in PAS](speciesSpecific.html)
##Differential Isoform Analysis:
* [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)
* [Explore nuclear differential APA PAS and genes](ExploredAPA.html)
* [Enrichment for differencial APA and eQTL](DapaineQTL.html)
* [Enrichment for differencial APA and apaQTL](dAPAandapaQTL.html)
* [Look at dAPA and genes from Dominant PAS analysis](DominatPASandDIffAPA.html)
* [Visualization for all Nuclear DAPA genes](visualizePASUsage.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)
* [Effect size correlations](correlationPhenos.html)
##Mediation
* [Normalize Nuclear Fraction](NormalizePheno_nuclear.html)
* [Normalize clusters from splicing analysis](normalizeClusters.html)
* [Mediation analysis](mediation.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
* [Human Total vs Nuclear Analysis](Human_TvN.html)
* [Chimp Total vs Nuclear Analysis](Chimp_TvN.html)
* [Dominant PAS in Total Fraction](dominantPAS_total.html)