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Showing :
kallisto
•
reset
4
votes
2
replies
1.5k
views
How to do DESeq2 on Kallisto Data
DESeq2
Kallisto
updated 10 months ago by
dsull
▴ 40 • written 10 months ago by
Aaliya
• 0
3
votes
7
replies
1.5k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
19 months ago
Yijing
• 0
0
votes
2
replies
1.2k
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
19 months ago
Yijing
• 0
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 2.0 years ago by
James W. MacDonald
67k • written 2.0 years ago by
Mikhail Biryukov
▴ 10
1
vote
2
replies
1.0k
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
2.1 years ago
cta
• 0
3
votes
3
replies
1.3k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
2.1 years ago
duhwa.lee
• 0
2
votes
1
reply
2.1k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
BioNovice247
• 0
0
votes
1
reply
839
views
Pseudoalignment for repetitive sequences
Kallisto
RNASeq
pseudoaligners
ShortTandemRepeats
updated 3.4 years ago by
James W. MacDonald
67k • written 3.4 years ago by
Shu Yi
• 0
0
votes
2
replies
3.6k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 4.1 years ago by
Michael Love
43k • written 4.1 years ago by
m93
• 0
1
vote
9
replies
3.4k
views
Importing Kallisto counts with tximport
tximport
Kallisto
H5Fopen
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
zroger499
• 0
0
votes
2
replies
2.0k
views
error in creating kallisto index
kallisto
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
biok0423
▴ 20
2
votes
4
replies
5.4k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
5.6 years ago • updated 4.7 years ago
Mozart
▴ 30
1
vote
1
reply
1.1k
views
tximport errors with h5 and tsv files
tximport
kallisto
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
sp21
• 0
0
votes
6
replies
1.7k
views
how to set offset matrix to Deseq2 differential analysis
deseq2
Kallisto
tximport
updated 5.5 years ago by
Michael Love
43k • written 5.5 years ago by
qwzhang0601
• 0
3
votes
1
reply
2.0k
views
Tximport and pseudo alignment with Kallisto
kallisto
tximport
deseq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
Mozart
▴ 30
0
votes
4
replies
2.8k
views
Error in H5Fopen with kallisto .h5 files
tximport
kallisto
rhdf5
5.7 years ago
uso2015
• 0
1
vote
5
replies
3.3k
views
tximport error with kallisto .h5 files
deseq2
kallisto
tximport
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
steve.standage
• 0
2
votes
3
replies
1.8k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport
kallisto
updated 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
Lucas Carey
▴ 40
6
votes
6
replies
2.6k
views
Kallisto output with DEXSeq
dexseq
kallisto
NH_tag
updated 6.2 years ago by
Alejandro Reyes
★ 1.9k • written 6.2 years ago by
j2h2k2
• 0
1
vote
4
replies
2.8k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2
rnaseq
kallisto
tximport
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
Yunlu Zhu
• 0
0
votes
1
reply
1.2k
views
Error with tximport on Kallisto .h5 data.
tximport
kallisto
bioconductor
rnaseq
6.9 years ago
srdjan.kasapovic0
• 0
2
votes
4
replies
2.7k
views
tximport of kallisto files
tximport
deseq2
kallisto
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
Clara
• 0
0
votes
0
replies
1.1k
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
7.1 years ago
ilyco
• 0
3
votes
3
replies
1.6k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto
deseq2
tximport
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
thibault.lorin34
▴ 20
0
votes
1
reply
1.5k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2
kallisto
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
deena
▴ 20
2
votes
2
replies
2.1k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport
kallisto
txdb.mmusculus.ucsc.mm10.knowngene
updated 7.5 years ago by
James W. MacDonald
67k • written 7.5 years ago by
Kaustav
• 0
0
votes
3
replies
2.2k
views
(very) conflicting results with DESeq2 between versions
deseq2
tximport
rnaseq
kallisto
R
updated 7.5 years ago by
Michael Love
43k • written 7.5 years ago by
birgittenilsson
• 0
0
votes
7
replies
2.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 3.1 years ago by
nicolette.sipperly
• 0 • written 7.5 years ago by
urjaswita
▴ 40
2
votes
5
replies
3.9k
views
unable to get tximport to work on data from kallisto
tximport
kallisto
updated 7.6 years ago by
Steve Lianoglou
★ 13k • written 7.6 years ago by
swamyvinny
▴ 10
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport
Kallisto
rna-seq
updated 7.8 years ago by
pablo_garcia05
▴ 20 • written 8.6 years ago by
cguzman.bioinformatics
▴ 10
1
vote
13
replies
15k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
8.3 years ago • updated 8.2 years ago
yjliu1127
• 0
31 results • Page
1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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