Showing : kallisto • reset
3
votes
2
replies
323
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 11 weeks ago by ▴ 30 • written 11 weeks ago by • 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
815
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
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 17 months ago by 65k • written 17 months ago by ▴ 10
1
vote
2
replies
783
views
error loading kallisto output in tximport
file.exists false kallisto tximport
17 months ago cta • 0
3
votes
3
replies
914
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 41k • written 2.5 years ago by • 0
0
votes
1
reply
675
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 2.8 years ago by 65k • written 2.8 years ago by • 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 41k • written 3.5 years ago by • 0
1
vote
9
replies
2.9k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
0
votes
2
replies
1.6k
views
error in creating kallisto index
kallisto
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 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
902
views
tximport errors with h5 and tsv files
tximport kallisto
updated 4.4 years ago by 41k • written 4.4 years ago by • 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 41k • written 4.9 years ago by • 0
3
votes
1
reply
1.7k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 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 41k • written 5.3 years ago by • 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 50k • written 5.3 years ago by ▴ 40
6
votes
6
replies
2.2k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 5.6 years ago by ★ 1.9k • written 5.6 years ago by • 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 41k • written 6.1 years ago by • 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 41k • written 6.4 years ago by • 0
0
votes
0
replies
946
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 41k • written 6.5 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2 kallisto
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 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 65k • written 6.9 years ago by • 0
0
votes
3
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2.0k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 6.9 years ago by 41k • written 6.9 years ago by • 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 • 0 • written 6.9 years ago by ▴ 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 ★ 13k • written 7.0 years ago by ▴ 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 ▴ 20 • written 8.0 years ago by ▴ 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
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Replies
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Votes
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
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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