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Showing :
Kallisto
•
reset
3
votes
2
replies
311
views
How to do DESeq2 on Kallisto Data
DESeq2
Kallisto
updated 11 weeks ago by
dsull
▴ 30 • written 11 weeks ago by
Aaliya
• 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
811
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
12 months ago • updated 11 months ago
Yijing
• 0
4
votes
3
replies
1.0k
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
1
vote
2
replies
779
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
17 months ago
cta
• 0
3
votes
3
replies
910
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
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
0
votes
1
reply
672
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
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
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
1
vote
1
reply
900
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
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
3
votes
1
reply
1.7k
views
Tximport and pseudo alignment with Kallisto
kallisto
tximport
deseq2
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Mozart
▴ 30
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
0
votes
4
replies
2.4k
views
Error in H5Fopen with kallisto .h5 files
tximport
kallisto
rhdf5
5.1 years ago
uso2015
• 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
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
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
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
1
reply
1.0k
views
Error with tximport on Kallisto .h5 data.
tximport
kallisto
bioconductor
rnaseq
6.3 years ago
srdjan.kasapovic0
• 0
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
0
replies
945
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
6.5 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 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
thibault.lorin34
▴ 20
0
votes
1
reply
1.3k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2
kallisto
updated 6.6 years ago by
Michael Love
41k • written 6.6 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 6.9 years ago by
James W. MacDonald
65k • written 6.9 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 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
birgittenilsson
• 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
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
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
31 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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