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Showing :
tximport
•
reset
2
votes
3
replies
794
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 8 months ago by
Vitor
• 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 months ago by
Michael Love
41k • written 8 months ago by
Christian
• 0
0
votes
4
replies
850
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 7 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
9 months ago
Ndimensional
▴ 20
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 5 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
3
votes
2
replies
546
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
mckinlee.salazar
• 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 6 months ago by
RLiu
▴ 40
2
votes
1
reply
639
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 11 months ago by
Michael Love
41k • written 11 months ago by
prangannathofficial
• 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
11 months ago
Yijing
• 0
0
votes
2
replies
191
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 29 days ago by
Michael Love
41k • written 29 days ago by
SG
• 0
0
votes
1
reply
592
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Yijing
• 0
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 8 weeks ago by
Michael Love
41k • written 16 months ago by
kiqbal
• 0
0
votes
2
replies
641
views
tximport error in reading salmon output files?
tximport
tximportData
updated 12 weeks ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
2
votes
1
reply
233
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
hemantcnaik
• 0
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 8 months ago by
k.vitting.seerup
▴ 120 • written 9 months ago by
elva.gypsophila
▴ 10
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 5 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
410
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
Kayleigh
• 0
0
votes
2
replies
144
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
21 days ago
Marianna
▴ 20
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2
sailfish
tximport
updated 11 months ago by
IUH
• 0 • written 6.8 years ago by
stan
• 0
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by
tangming2005
▴ 190 • written 3.8 years ago by
Ina Hoeschele
▴ 620
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by
Michael Love
41k • written 2.5 years ago by
nicolette.sipperly
• 0
0
votes
2
replies
811
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
12 months ago • updated 11 months ago
Yijing
• 0
0
votes
1
reply
319
views
tximport error with rsem files
rsem
tximport
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
apolitics
• 0
25 results • Page
1 of 1
Recent ...
Replies
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Votes
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?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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