Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
kallisto
•
reset
4
votes
2
replies
1.6k
views
How to do DESeq2 on Kallisto Data
DESeq2
Kallisto
updated 11 months ago by
dsull
▴ 40 • written 11 months ago by
Aaliya
• 0
3
votes
7
replies
1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
20 months ago
Yijing
• 0
0
votes
2
replies
1.3k
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
20 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 2.1 years ago by
James W. MacDonald
67k • written 2.1 years ago by
Mikhail Biryukov
▴ 10
1
vote
2
replies
1.1k
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
2.2 years ago
cta
• 0
3
votes
3
replies
1.4k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
2.2 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 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
BioNovice247
• 0
0
votes
1
reply
868
views
Pseudoalignment for repetitive sequences
Kallisto
RNASeq
pseudoaligners
ShortTandemRepeats
updated 3.5 years ago by
James W. MacDonald
67k • written 3.5 years ago by
Shu Yi
• 0
0
votes
2
replies
3.7k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 4.2 years ago by
Michael Love
43k • written 4.2 years ago by
m93
• 0
1
vote
9
replies
3.4k
views
Importing Kallisto counts with tximport
tximport
Kallisto
H5Fopen
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
zroger499
• 0
0
votes
2
replies
2.0k
views
error in creating kallisto index
kallisto
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
biok0423
▴ 20
2
votes
4
replies
5.5k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
5.7 years ago • updated 4.8 years ago
Mozart
▴ 30
1
vote
1
reply
1.1k
views
tximport errors with h5 and tsv files
tximport
kallisto
updated 5.1 years ago by
Michael Love
43k • written 5.1 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 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
qwzhang0601
• 0
3
votes
1
reply
2.1k
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
5.8 years ago
uso2015
• 0
1
vote
5
replies
3.3k
views
tximport error with kallisto .h5 files
deseq2
kallisto
tximport
updated 6.0 years ago by
Michael Love
43k • written 6.0 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 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
Lucas Carey
▴ 40
6
votes
6
replies
2.7k
views
Kallisto output with DEXSeq
dexseq
kallisto
NH_tag
updated 6.3 years ago by
Alejandro Reyes
★ 1.9k • written 6.3 years ago by
j2h2k2
• 0
1
vote
4
replies
2.9k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2
rnaseq
kallisto
tximport
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Yunlu Zhu
• 0
0
votes
1
reply
1.2k
views
Error with tximport on Kallisto .h5 data.
tximport
kallisto
bioconductor
rnaseq
7.0 years ago
srdjan.kasapovic0
• 0
2
votes
4
replies
2.8k
views
tximport of kallisto files
tximport
deseq2
kallisto
updated 7.1 years ago by
Michael Love
43k • written 7.1 years ago by
Clara
• 0
0
votes
0
replies
1.1k
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
7.2 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
1.6k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2
kallisto
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
deena
▴ 20
2
votes
2
replies
2.2k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport
kallisto
txdb.mmusculus.ucsc.mm10.knowngene
updated 7.6 years ago by
James W. MacDonald
67k • written 7.6 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 7.6 years ago by
Michael Love
43k • written 7.6 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 3.2 years ago by
nicolette.sipperly
• 0 • written 7.6 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 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 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 7.9 years ago by
pablo_garcia05
▴ 20 • written 8.7 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
yjliu1127
• 0
31 results • Page
1 of 1
Recent ...
Replies
Comment: EuroBioC2023 abstract submission closing soon!
by
Jeremy
• 0
Thanks for the reminder! If you're a Bioconductor user or developer, make sure to [tabs][1] submit your abstract by the deadline, Monday, A…
Comment: Mean variance curve troubleshoot filtering
by
gingergeiger22
• 0
Gordon, thank for your response. 'filterByExpr()' was marginally better. I can see high variability in samples within the groups from the M…
Comment: What is the importance of `--countReadPairs` in featureCounts on paired end data
by
rohitsatyam102
▴ 20
Since I don't know which organism you are working on, I would recommend using the following: `-s 0` if library is unstranded `-C` Discard…
Comment: What is the importance of `--countReadPairs` in featureCounts on paired end data
by
rohitsatyam102
▴ 20
Yes use this option. It is recommended for PE and if you don't use it you will observe nearly twice the number of counts in your results. H…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
• 0
I edited the previous post. I meant to remove the estimateGLMRobustDisp line in the second snipper : ```` DGE_list_object <- estimateGLMR…
Votes
Comment: Comparing different method for DESEQ2
Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
Awards
• All
Popular Question
to
Ken C
• 0
Popular Question
to
gingergeiger22
• 0
Popular Question
to
Gordon Smyth
52k
Popular Question
to
James W. MacDonald
67k
Popular Question
to
Chris
▴ 20
Locations
• All
Macao,
1 hour ago
Taiwan,
1 hour ago
United States,
1 hour ago
China,
1 hour ago
Australia,
1 hour ago
Traffic: 631 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6