Showing : sgseq • reset
0
votes
0
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16
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Differential splicing from SGSeq analysis
DEXSeq SGSeq
1 day ago Sara • 0
0
votes
1
reply
121
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 9 days ago by • 0 • written 14 days ago by • 0
0
votes
0
replies
144
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Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag SplicedAlignment SGSeq minimap2
7 weeks ago jk • 0
0
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0
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245
views
SGSeq how export PSI values for each typr of splice variant
SGSeq
5 months ago Alison • 0
1
vote
4
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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 ▴ 180 • written 3.5 years ago by ▴ 10
5
votes
8
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3.0k
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Issues with SGSeq: analyzeFeatures() returns errors on BAM files
sgseq
updated 4.4 years ago by • 0 • written 7.7 years ago by ▴ 80
0
votes
1
reply
710
views
Extract sample information from own BAM files using SGSeq
SGSeq
updated 4.4 years ago by ▴ 180 • written 4.4 years ago by • 0
3
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3
replies
872
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Custom gene annotations for SGSeq
sgseq alternative splicing rna seq
updated 4.4 years ago by ▴ 180 • written 4.4 years ago by • 0
0
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2
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768
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using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq SGSeq Alternative splicing
updated 4.5 years ago by ▴ 180 • written 4.5 years ago by • 0
0
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0
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843
views
How to run my own data using SGSeq?
annotation sgseq
updated 5.2 years ago by 3.8k • written 5.2 years ago by • 0
0
votes
6
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1.5k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
5.5 years ago andrea.bast • 0
0
votes
1
reply
915
views
SGFeatureCounts function in SGSeq package failed to generate splice graphs
sgseq
updated 6.5 years ago by ▴ 180 • written 6.5 years ago by • 0
1
vote
1
reply
1.6k
views
SGSeq error on getBamInfo
SGSeq getBamInfo RNASeq
updated 6.6 years ago by ▴ 180 • written 6.6 years ago by ▴ 10
4
votes
5
replies
1.5k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 6.6 years ago by ▴ 180 • written 6.6 years ago by ▴ 10
8
votes
4
replies
1.6k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 6.7 years ago by ▴ 180 • written 6.7 years ago by ▴ 80
0
votes
3
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1.1k
views
question about subsetting SGSeq results by different categories of splice events
sgseq
updated 6.8 years ago by ▴ 180 • written 6.8 years ago by • 0
0
votes
5
replies
1.6k
views
Error when running getSGFeatureCounts
SGSeq software error
updated 7.2 years ago by ▴ 180 • written 7.2 years ago by • 0
0
votes
15
replies
2.1k
views
Issues with SGSeq: analyzeVariants method returns an error...
sgseq analyzevariants
updated 7.4 years ago by ▴ 180 • written 7.6 years ago by ▴ 80
1
vote
15
replies
3.2k
views
Issues with SGSeq: plotFeatures method returns NULL
sgseq
updated 7.6 years ago by ▴ 180 • written 7.7 years ago by ▴ 80
3
votes
16
replies
2.6k
views
Read counts generated by SGSeq are always 0
sgseq splicing alternative splicing
updated 8.2 years ago by ▴ 180 • written 8.2 years ago by ▴ 10
2
votes
2
replies
1.6k
views
SGSeq: class of "sample_info" argument of analyzeFeatures, data.frame or DataFrame!
sgseq
updated 8.2 years ago by ▴ 180 • written 8.2 years ago by ▴ 40
1
vote
6
replies
1.9k
views
Error when predicting features with SGSeq
SGSeq
updated 8.8 years ago by ▴ 80 • written 8.8 years ago by ▴ 150
1
vote
6
replies
2.1k
views
SGSeq error on analyzeFeatures
SGSeq analyzeFeatures Splicing
9.4 years ago • updated 9.3 years ago Paolo Guarnieri ▴ 20
23 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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