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Showing :
Kallisto
•
reset
3
votes
2
replies
296
views
How to do DESeq2 on Kallisto Data
DESeq2
Kallisto
updated 10 weeks ago by
dsull
▴ 30 • written 10 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
801
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
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
769
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
17 months ago
cta
• 0
3
votes
3
replies
898
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
668
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
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
1
vote
1
reply
895
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
1.3k
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
0
votes
4
replies
2.3k
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 5.5 years ago by
Alejandro Reyes
★ 1.9k • written 5.5 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
933
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 6.9 years ago by
Steve Lianoglou
★ 13k • written 6.9 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 8.0 years ago by
cguzman.bioinformatics
▴ 10
1
vote
13
replies
14k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
7.6 years ago
yjliu1127
• 0
31 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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