Showing : recount3 • reset
8
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8
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251
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Counts from recount3 for DESeq2 analysis
recount3 DESeq2
5 weeks ago william.benit ▴ 10
0
votes
2
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142
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Missing sample in recount3 data
recount3
9 weeks ago • updated 27 days ago alex.dietrich • 0
0
votes
1
reply
124
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Retrieve the read counts per transcript instead of per gene
recount3
updated 7 weeks ago by ▴ 980 • written 9 weeks ago by ▴ 10
11
votes
8
replies
830
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Error when downloading data with recount3.
recount3
updated 7 weeks ago by ▴ 40 • written 19 months ago by ▴ 20
1
vote
1
reply
159
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recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 8 weeks ago by ▴ 980 • written 8 weeks ago by ▴ 10
0
votes
1
reply
132
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Sample tissue annotation
recount3
updated 12 weeks ago by ▴ 980 • written 3 months ago by • 0
0
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1
reply
219
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Distinguishing between single cell and bulk data in recount3 study explorer
recount3
updated 12 weeks ago by ▴ 980 • written 5 months ago by • 0
0
votes
2
replies
334
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Get read counts for TCGA samples via recount3
recount3
6 months ago mario.keller.1988 ▴ 10
2
votes
2
replies
265
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[recount3] Merge gene counts tables from multiple projects (SRP)
recount3 recountWorkflow
updated 7 months ago by ▴ 980 • written 7 months ago by ▴ 480
0
votes
1
reply
193
views
Different read support for splice junctions using snapcount and recount3
recount3 snapcount
updated 7 months ago by ▴ 980 • written 7 months ago by ▴ 10
2
votes
3
replies
363
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Downloading count matrix for full recount3 dataset
recount3
10 months ago Ben • 0
0
votes
2
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416
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recount3: advice for working with an unannotated genes
recount3
updated 6 months ago by • 0 • written 12 months ago by • 0
1
vote
1
reply
413
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Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 11 months ago by ▴ 980 • written 12 months ago by ▴ 10
0
votes
1
reply
492
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Using recount data to calculate Intron retention
snapcount recount3 recount
updated 14 months ago by ▴ 980 • written 14 months ago by • 0
14 results • Page 1 of 1
Recent ...
Replies
Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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