hbctraining DGE_workshop_salmon issues

hbctraining / DGE_workshop_salmon

https://hbctraining.github.io/DGE_workshop_salmon/

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Add link to Mike Love's new book

#53 marypiper opened 4 years ago
0
update likelihood ratio definition

#52 mistrm82 closed 4 years ago
1
WGCNA package link not working

#51 jihe-liu closed 4 years ago
1
change linked file in FA lesson

#50 mistrm82 closed 4 years ago
1
do we set lfcThreshold in results or lfcShrink or both?

#49 mistrm82 opened 4 years ago
0
update a markdown report link

#48 mistrm82 closed 4 years ago
1
PCA link not working

#47 jihe-liu opened 4 years ago
0
Fixed typo on line 35

#46 kant closed 4 years ago
0
Run through functional analysis

#45 mistrm82 closed 4 years ago
2
shorten the overview lesson (01)

#44 mistrm82 closed 4 years ago
0
Reduce GO and add table of databases

#43 rkhetani opened 4 years ago
0
make this a 1.5 day workshop?

#42 mistrm82 opened 4 years ago
1
coef vs contrast?

#41 mistrm82 opened 4 years ago
2
Include a note about detach() getting an error if dpylr is not attached

#40 marypiper closed 4 years ago
1
Shorten annotations to not including Annotationdbi

#39 marypiper closed 4 years ago
2
Add exercises to make workshop more interactive - especially for functional analysis

#38 marypiper closed 4 years ago
1
Discussion of possibly shortening Annotation session in the workshop

#37 jihe-liu closed 4 years ago
1
Extract annotations of interest: more explanation

#36 jihe-liu closed 4 years ago
1
AnnotationHub() note

#35 jihe-liu closed 4 years ago
1
update FA lesson for SPIA

#34 mistrm82 closed 4 years ago
2
Change to log2FC shrinkage to apeglm following advice in Mike

#33 marypiper opened 4 years ago
2
Update workflow image with log2FC shrinkage after DE testing

#32 marypiper opened 4 years ago
1
change the wording of refresher boxplot question

#31 mistrm82 closed 4 years ago
2
reg exp for extracting salmon files

#30 jihe-liu closed 4 years ago
1
set.seed()

#29 marypiper closed 4 years ago
0
Syntax issue on line 35

#28 kant closed 4 years ago
0
add an instance of using save() and load()

#27 rkhetani closed 4 years ago
2
reduce some text in the Annotation lesson

#26 mistrm82 closed 4 years ago
0
changing to AnnotationHub

#25 mistrm82 closed 4 years ago
2
clusterprofiler arguments

#24 rkhetani closed 4 years ago
2
An explanation for why the AnnotationDbi has so many more genes

#23 mistrm82 closed 4 years ago
1
Change image of RNA composition to reflect fewer reads in the OE sample (sample A)

#22 marypiper closed 4 years ago
1
mean-variance plot

#21 marypiper closed 5 years ago
1
change back to vst from rld?

#20 marypiper closed 4 years ago
1
Reorder Wald test lesson

#19 marypiper closed 4 years ago
0
Add figure for independent filtering

#18 marypiper closed 4 years ago
2
change the scales of mean versus variance plot

#17 mistrm82 closed 4 years ago
1
Add a link in QC lesson to single cell materials

#16 mistrm82 closed 4 years ago
2
Apply to map?

#15 rkhetani closed 4 years ago
1
Add note about ignoreTxVersion = TRUE

#14 marypiper closed 4 years ago
1
adjust timings for Wald test and R refresher

#13 marypiper closed 5 years ago
1
reduce viz lesson

#12 rkhetani closed 5 years ago
1
Arguments and functions each on own line and comment all code chunks

#11 marypiper opened 5 years ago
3
Wald test lesson (05_ - Meeta)

#10 marypiper closed 5 years ago
0
Shorten GO part of functional analysis and some of the code (MP)

#9 marypiper opened 5 years ago
1
Remove design <- ~ age + treat_sex part of the design formula (MP)

#8 marypiper closed 5 years ago
1
Dispersion - consolidate some of the descriptions (MP)

#7 marypiper closed 4 years ago
0
FA - assess what impact changing AnnotationDbi to AnnotationHub

#6 marypiper closed 4 years ago
2
apply -> map

#5 rkhetani closed 4 years ago
1
fix small typo

#4 rkhetani closed 4 years ago
2