Showing : sgseq • reset
10
votes
11
replies
2.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 months ago by • 0 • written 7.1 years ago by ▴ 80
0
votes
0
replies
255
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
5 months ago Sara • 0
1
vote
1
reply
310
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 5 months ago by • 0 • written 6 months ago by • 0
1
vote
0
replies
440
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag SplicedAlignment SGSeq minimap2
7 months ago jk ▴ 10
0
votes
0
replies
396
views
SGSeq how export PSI values for each typr of splice variant
SGSeq
11 months ago Alison • 0
2
votes
5
replies
1.5k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq limma edgeR
updated 5 weeks ago by • 0 • written 4.0 years ago by ▴ 10
6
votes
8
replies
3.4k
views
Issues with SGSeq: analyzeFeatures() returns errors on BAM files
sgseq
updated 4.8 years ago by ▴ 10 • written 8.2 years ago by ▴ 80
2
votes
1
reply
959
views
Extract sample information from own BAM files using SGSeq
SGSeq
updated 4.9 years ago by ▴ 260 • written 4.9 years ago by ▴ 10
4
votes
4
replies
1.1k
views
Custom gene annotations for SGSeq
sgseq alternative splicing rna seq
updated 10 weeks ago by • 0 • written 4.9 years ago by • 0
0
votes
2
replies
928
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq SGSeq Alternative splicing
updated 5.0 years ago by ▴ 260 • written 5.0 years ago by • 0
0
votes
0
replies
949
views
How to run my own data using SGSeq?
annotation sgseq
updated 5.7 years ago by 4.0k • written 5.7 years ago by • 0
0
votes
6
replies
1.7k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
6.0 years ago • updated 5.9 years ago andrea.bast • 0
0
votes
1
reply
1.1k
views
SGFeatureCounts function in SGSeq package failed to generate splice graphs
sgseq
updated 7.0 years ago by ▴ 260 • written 7.0 years ago by • 0
2
votes
1
reply
1.8k
views
SGSeq error on getBamInfo
SGSeq getBamInfo RNASeq
updated 7.0 years ago by ▴ 260 • written 7.0 years ago by ▴ 40
4
votes
5
replies
1.8k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 7.0 years ago by ▴ 260 • written 7.1 years ago by ▴ 40
3
votes
3
replies
1.7k
views
question about subsetting SGSeq results by different categories of splice events
sgseq
updated 7.3 years ago by ▴ 260 • written 7.3 years ago by ▴ 10
1
vote
5
replies
1.8k
views
Error when running getSGFeatureCounts
SGSeq software error
updated 7.7 years ago by ▴ 260 • written 7.7 years ago by ▴ 10
0
votes
15
replies
2.4k
views
Issues with SGSeq: analyzeVariants method returns an error...
sgseq analyzevariants
updated 7.9 years ago by ▴ 260 • written 8.0 years ago by ▴ 80
1
vote
15
replies
3.6k
views
Issues with SGSeq: plotFeatures method returns NULL
sgseq
updated 8.0 years ago by ▴ 260 • written 8.2 years ago by ▴ 80
5
votes
16
replies
3.0k
views
Read counts generated by SGSeq are always 0
sgseq splicing alternative splicing
updated 8.6 years ago by ▴ 260 • written 8.6 years ago by ▴ 20
2
votes
2
replies
1.7k
views
SGSeq: class of "sample_info" argument of analyzeFeatures, data.frame or DataFrame!
sgseq
updated 8.6 years ago by ▴ 260 • written 8.6 years ago by ▴ 40
1
vote
6
replies
2.1k
views
Error when predicting features with SGSeq
SGSeq
updated 9.2 years ago by ▴ 90 • written 9.2 years ago by ▴ 150
1
vote
6
replies
2.4k
views
SGSeq error on analyzeFeatures
SGSeq analyzeFeatures Splicing
9.8 years ago Paolo Guarnieri ▴ 20
23 results • Page 1 of 1
Recent ...
Replies
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file by James W. MacDonald 67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Comment: Are transformed values from rlog /vst log2 normalized counts? by James W. MacDonald 67k
The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
Many thanks for you detailed answer, I really appreciate it. Could you give me an example (or more if possible) of analysis using count-b…
Votes
Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
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