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SGSeq
•
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0
votes
0
replies
104
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
27 days ago
jk
• 0
0
votes
0
replies
228
views
SGSeq how export PSI values for each typr of splice variant
SGSeq
4 months ago
Alison
• 0
0
votes
4
replies
1.1k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq
limma
edgeR
updated 3.5 years ago by
Leonard Goldstein
▴ 150 • written 3.5 years ago by
zliu
• 0
3
votes
8
replies
3.0k
views
Issues with SGSeq: analyzeFeatures() returns errors on BAM files
sgseq
updated 4.3 years ago by
anjanhazra
• 0 • written 7.6 years ago by
Sylvain Foisy
▴ 50
0
votes
1
reply
693
views
Extract sample information from own BAM files using SGSeq
SGSeq
updated 4.3 years ago by
Leonard Goldstein
▴ 150 • written 4.3 years ago by
anjanhazra
• 0
3
votes
3
replies
838
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 4.3 years ago by
Leonard Goldstein
▴ 150 • written 4.3 years ago by
116100016
• 0
0
votes
2
replies
744
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 4.4 years ago by
Leonard Goldstein
▴ 150 • written 4.4 years ago by
116100016
• 0
0
votes
0
replies
822
views
How to run my own data using SGSeq?
annotation
sgseq
updated 5.2 years ago by
shepherl
3.8k • written 5.2 years ago by
huizeng
• 0
0
votes
6
replies
1.5k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq
alternative splicing
SGSeq
5.4 years ago
andrea.bast
• 0
0
votes
1
reply
890
views
SGFeatureCounts function in SGSeq package failed to generate splice graphs
sgseq
updated 6.4 years ago by
Leonard Goldstein
▴ 150 • written 6.4 years ago by
mgdrnl
• 0
1
vote
1
reply
1.6k
views
SGSeq error on getBamInfo
SGSeq
getBamInfo
RNASeq
updated 6.5 years ago by
Leonard Goldstein
▴ 150 • written 6.5 years ago by
oolongoni
▴ 10
3
votes
5
replies
1.5k
views
R session crash with SGSeq::convertToTxFeatures
crash
SGSeq
TxDb
makeTxDbFromBiomart
TxFeatures
updated 6.5 years ago by
Leonard Goldstein
▴ 150 • written 6.5 years ago by
oolongoni
▴ 10
6
votes
4
replies
1.5k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 6.6 years ago by
Leonard Goldstein
▴ 150 • written 6.6 years ago by
Sylvain Foisy
▴ 50
0
votes
3
replies
1.1k
views
question about subsetting SGSeq results by different categories of splice events
sgseq
updated 6.8 years ago by
Leonard Goldstein
▴ 150 • written 6.8 years ago by
amanda.joy.price
• 0
0
votes
5
replies
1.6k
views
Error when running getSGFeatureCounts
SGSeq
software error
updated 7.1 years ago by
Leonard Goldstein
▴ 150 • written 7.1 years ago by
jpromero
• 0
0
votes
15
replies
2.0k
views
Issues with SGSeq: analyzeVariants method returns an error...
sgseq
analyzevariants
updated 7.3 years ago by
Leonard Goldstein
▴ 150 • written 7.5 years ago by
Sylvain Foisy
▴ 50
0
votes
15
replies
3.1k
views
Issues with SGSeq: plotFeatures method returns NULL
sgseq
updated 7.5 years ago by
Leonard Goldstein
▴ 150 • written 7.6 years ago by
Sylvain Foisy
▴ 50
3
votes
16
replies
2.5k
views
Read counts generated by SGSeq are always 0
sgseq
splicing
alternative splicing
updated 8.1 years ago by
Leonard Goldstein
▴ 150 • written 8.1 years ago by
vakul.mohanty
▴ 10
2
votes
2
replies
1.5k
views
SGSeq: class of "sample_info" argument of analyzeFeatures, data.frame or DataFrame!
sgseq
updated 8.1 years ago by
Leonard Goldstein
▴ 150 • written 8.1 years ago by
Chao-Jen Wong
▴ 30
0
votes
6
replies
1.8k
views
Error when predicting features with SGSeq
SGSeq
updated 8.7 years ago by
Leonard Goldstein
▴ 70 • written 8.7 years ago by
Helen Zhou
▴ 140
0
votes
6
replies
2.1k
views
SGSeq error on analyzeFeatures
SGSeq
analyzeFeatures
Splicing
9.3 years ago
Paolo Guarnieri
▴ 20
21 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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by
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This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
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by
James W. MacDonald
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It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
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50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
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DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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Circumvent creating .ff files in the working directory when using genotype.Illumina() function
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