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Showing :
kallisto
•
reset
3
votes
2
replies
447
views
How to do DESeq2 on Kallisto Data
DESeq2
Kallisto
updated 3 months ago by
dsull
▴ 30 • written 3 months ago by
Aaliya
• 0
3
votes
7
replies
1.2k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
12 months ago
Yijing
• 0
0
votes
2
replies
863
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
13 months ago • updated 12 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 18 months ago by
James W. MacDonald
66k • written 18 months ago by
Mikhail Biryukov
▴ 10
1
vote
2
replies
814
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
18 months ago
cta
• 0
3
votes
3
replies
970
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
19 months ago • updated 18 months ago
duhwa.lee
• 0
2
votes
1
reply
1.7k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 2.6 years ago by
Michael Love
42k • written 2.6 years ago by
BioNovice247
• 0
0
votes
1
reply
688
views
Pseudoalignment for repetitive sequences
Kallisto
RNASeq
pseudoaligners
ShortTandemRepeats
updated 2.9 years ago by
James W. MacDonald
66k • written 2.9 years ago by
Shu Yi
• 0
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 3.6 years ago by
Michael Love
42k • written 3.6 years ago by
m93
• 0
1
vote
9
replies
3.0k
views
Importing Kallisto counts with tximport
tximport
Kallisto
H5Fopen
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
zroger499
• 0
0
votes
2
replies
1.6k
views
error in creating kallisto index
kallisto
updated 4.1 years ago by
Michael Love
42k • written 4.1 years ago by
biok0423
▴ 20
2
votes
4
replies
4.7k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
5.1 years ago • updated 4.2 years ago
Mozart
▴ 30
1
vote
1
reply
931
views
tximport errors with h5 and tsv files
tximport
kallisto
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
sp21
• 0
0
votes
6
replies
1.4k
views
how to set offset matrix to Deseq2 differential analysis
deseq2
Kallisto
tximport
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
qwzhang0601
• 0
3
votes
1
reply
1.8k
views
Tximport and pseudo alignment with Kallisto
kallisto
tximport
deseq2
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Mozart
▴ 30
0
votes
4
replies
2.4k
views
Error in H5Fopen with kallisto .h5 files
tximport
kallisto
rhdf5
5.2 years ago
uso2015
• 0
1
vote
5
replies
2.9k
views
tximport error with kallisto .h5 files
deseq2
kallisto
tximport
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
steve.standage
• 0
2
votes
3
replies
1.6k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport
kallisto
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
Lucas Carey
▴ 40
6
votes
6
replies
2.3k
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
1
vote
4
replies
2.6k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2
rnaseq
kallisto
tximport
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
Yunlu Zhu
• 0
0
votes
1
reply
1.1k
views
Error with tximport on Kallisto .h5 data.
tximport
kallisto
bioconductor
rnaseq
6.4 years ago
srdjan.kasapovic0
• 0
2
votes
4
replies
2.5k
views
tximport of kallisto files
tximport
deseq2
kallisto
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
Clara
• 0
0
votes
0
replies
981
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
6.6 years ago
ilyco
• 0
3
votes
3
replies
1.4k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto
deseq2
tximport
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
thibault.lorin34
▴ 20
0
votes
1
reply
1.3k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2
kallisto
updated 6.7 years ago by
Michael Love
42k • written 6.7 years ago by
deena
▴ 20
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 7.0 years ago by
James W. MacDonald
66k • written 7.0 years ago by
Kaustav
• 0
0
votes
3
replies
2.0k
views
(very) conflicting results with DESeq2 between versions
deseq2
tximport
rnaseq
kallisto
R
updated 7.0 years ago by
Michael Love
42k • written 7.0 years ago by
birgittenilsson
• 0
0
votes
7
replies
2.5k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto
tximport
RNA-Seq
across species
updated 2.6 years ago by
nicolette.sipperly
• 0 • written 7.0 years ago by
urjaswita
▴ 40
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
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 8.1 years ago by
cguzman.bioinformatics
▴ 10
1
vote
13
replies
14k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
7.7 years ago
yjliu1127
• 0
31 results • Page
1 of 1
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function
by
Robert Castelo
★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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Robert Castelo
★ 3.3k
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to
kevin.rue
▴ 350
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to
Wei Shi
★ 3.6k
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to
Gordon Smyth
50k
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to
jovel_juan
▴ 30
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