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Kallisto
•
reset
1
vote
13
replies
14k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
7.6 years ago
yjliu1127
• 0
9
votes
11
replies
5.6k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport
Kallisto
rna-seq
updated 7.2 years ago by
pablo_garcia05
▴ 20 • written 8.0 years ago by
cguzman.bioinformatics
▴ 10
2
votes
4
replies
4.6k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
5.0 years ago • updated 4.1 years ago
Mozart
▴ 30
2
votes
5
replies
3.6k
views
unable to get tximport to work on data from kallisto
tximport
kallisto
updated 7.0 years ago by
Steve Lianoglou
★ 13k • written 7.0 years ago by
swamyvinny
▴ 10
0
votes
2
replies
3.1k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
m93
• 0
1
vote
9
replies
2.9k
views
Importing Kallisto counts with tximport
tximport
Kallisto
H5Fopen
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
zroger499
• 0
1
vote
5
replies
2.9k
views
tximport error with kallisto .h5 files
deseq2
kallisto
tximport
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
steve.standage
• 0
1
vote
4
replies
2.5k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2
rnaseq
kallisto
tximport
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
Yunlu Zhu
• 0
0
votes
7
replies
2.4k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 2.5 years ago by
nicolette.sipperly
• 0 • written 6.9 years ago by
urjaswita
▴ 40
2
votes
4
replies
2.4k
views
tximport of kallisto files
tximport
deseq2
kallisto
updated 6.4 years ago by
Michael Love
41k • written 6.4 years ago by
Clara
• 0
0
votes
4
replies
2.4k
views
Error in H5Fopen with kallisto .h5 files
tximport
kallisto
rhdf5
5.1 years ago
uso2015
• 0
6
votes
6
replies
2.2k
views
Kallisto output with DEXSeq
dexseq
kallisto
NH_tag
updated 5.6 years ago by
Alejandro Reyes
★ 1.9k • written 5.6 years ago by
j2h2k2
• 0
0
votes
3
replies
2.0k
views
(very) conflicting results with DESeq2 between versions
deseq2
tximport
rnaseq
kallisto
R
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
birgittenilsson
• 0
2
votes
2
replies
1.9k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport
kallisto
txdb.mmusculus.ucsc.mm10.knowngene
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
Kaustav
• 0
3
votes
1
reply
1.7k
views
Tximport and pseudo alignment with Kallisto
kallisto
tximport
deseq2
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
Mozart
▴ 30
0
votes
2
replies
1.6k
views
error in creating kallisto index
kallisto
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
biok0423
▴ 20
2
votes
1
reply
1.6k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
BioNovice247
• 0
2
votes
3
replies
1.5k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport
kallisto
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
Lucas Carey
▴ 40
3
votes
3
replies
1.4k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto
deseq2
tximport
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
thibault.lorin34
▴ 20
0
votes
6
replies
1.4k
views
how to set offset matrix to Deseq2 differential analysis
deseq2
Kallisto
tximport
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
qwzhang0601
• 0
0
votes
1
reply
1.3k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2
kallisto
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
deena
▴ 20
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
12 months ago • updated 11 months ago
Yijing
• 0
4
votes
3
replies
1.1k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Mikhail Biryukov
▴ 10
0
votes
1
reply
1.0k
views
Error with tximport on Kallisto .h5 data.
tximport
kallisto
bioconductor
rnaseq
6.3 years ago
srdjan.kasapovic0
• 0
0
votes
0
replies
951
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
6.5 years ago
ilyco
• 0
3
votes
3
replies
918
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
18 months ago • updated 17 months ago
duhwa.lee
• 0
1
vote
1
reply
906
views
tximport errors with h5 and tsv files
tximport
kallisto
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
sp21
• 0
0
votes
2
replies
816
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
12 months ago
Yijing
• 0
1
vote
2
replies
785
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
17 months ago
cta
• 0
0
votes
1
reply
675
views
Pseudoalignment for repetitive sequences
Kallisto
RNASeq
pseudoaligners
ShortTandemRepeats
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
Shu Yi
• 0
3
votes
2
replies
325
views
How to do DESeq2 on Kallisto Data
DESeq2
Kallisto
updated 11 weeks ago by
dsull
▴ 30 • written 11 weeks ago by
Aaliya
• 0
31 results • Page
1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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