Showing : sgseq • reset
10
votes
11
replies
3.3k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 19 months ago by • 0 • written 8.3 years ago by ▴ 80
0
votes
0
replies
565
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
20 months ago • updated 19 months ago Sara • 0
1
vote
1
reply
684
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 20 months ago by • 0 • written 20 months ago by • 0
1
vote
0
replies
771
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag SplicedAlignment SGSeq minimap2
21 months ago jk ▴ 10
0
votes
0
replies
612
views
SGSeq how export PSI values for each typr of splice variant
SGSeq
2.1 years ago Alison • 0
2
votes
5
replies
2.0k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq limma edgeR
updated 15 months ago by • 0 • written 5.2 years ago by ▴ 10
6
votes
8
replies
4.1k
views
Issues with SGSeq: analyzeFeatures() returns errors on BAM files
sgseq
updated 6.0 years ago by ▴ 10 • written 9.4 years ago by ▴ 80
2
votes
1
reply
1.2k
views
Extract sample information from own BAM files using SGSeq
SGSeq
updated 6.0 years ago by ▴ 260 • written 6.0 years ago by ▴ 10
4
votes
4
replies
1.5k
views
Custom gene annotations for SGSeq
sgseq alternative splicing rna seq
updated 16 months ago by • 0 • written 6.1 years ago by • 0
0
votes
2
replies
1.4k
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq SGSeq Alternative splicing
updated 6.2 years ago by ▴ 260 • written 6.2 years ago by • 0
0
votes
0
replies
1.2k
views
How to run my own data using SGSeq?
annotation sgseq
updated 6.9 years ago by 4.2k • written 6.9 years ago by • 0
0
votes
6
replies
2.2k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
7.1 years ago andrea.bast • 0
0
votes
1
reply
1.4k
views
SGFeatureCounts function in SGSeq package failed to generate splice graphs
sgseq
updated 8.2 years ago by ▴ 260 • written 8.2 years ago by • 0
2
votes
1
reply
2.1k
views
SGSeq error on getBamInfo
SGSeq getBamInfo RNASeq
updated 8.2 years ago by ▴ 260 • written 8.2 years ago by ▴ 40
4
votes
5
replies
2.2k
views
R session crash with SGSeq::convertToTxFeatures
crash SGSeq TxDb makeTxDbFromBiomart TxFeatures
updated 8.2 years ago by ▴ 260 • written 8.2 years ago by ▴ 40
3
votes
3
replies
2.1k
views
question about subsetting SGSeq results by different categories of splice events
sgseq
updated 8.5 years ago by ▴ 260 • written 8.5 years ago by ▴ 10
1
vote
5
replies
2.1k
views
Error when running getSGFeatureCounts
SGSeq software error
updated 8.9 years ago by ▴ 260 • written 8.9 years ago by ▴ 10
0
votes
15
replies
3.3k
views
Issues with SGSeq: analyzeVariants method returns an error...
sgseq analyzevariants
updated 9.0 years ago by ▴ 260 • written 9.2 years ago by ▴ 80
1
vote
15
replies
4.6k
views
Issues with SGSeq: plotFeatures method returns NULL
sgseq
updated 9.2 years ago by ▴ 260 • written 9.4 years ago by ▴ 80
5
votes
16
replies
3.7k
views
Read counts generated by SGSeq are always 0
sgseq splicing alternative splicing
updated 9.8 years ago by ▴ 260 • written 9.8 years ago by ▴ 20
2
votes
2
replies
1.9k
views
SGSeq: class of "sample_info" argument of analyzeFeatures, data.frame or DataFrame!
sgseq
updated 9.8 years ago by ▴ 260 • written 9.8 years ago by ▴ 40
1
vote
6
replies
2.5k
views
Error when predicting features with SGSeq
SGSeq
updated 10.4 years ago by ▴ 90 • written 10.4 years ago by ▴ 150
1
vote
6
replies
2.9k
views
SGSeq error on analyzeFeatures
SGSeq analyzeFeatures Splicing
11.0 years ago Paolo Guarnieri ▴ 20
23 results • Page 1 of 1
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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