Showing : Kallisto • reset
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
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
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
0
votes
7
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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
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
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
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
2
votes
4
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2.4k
views
tximport of kallisto files
tximport deseq2 kallisto
updated 6.4 years ago by 41k • written 6.4 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
6
votes
6
replies
2.2k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 5.5 years ago by ★ 1.9k • written 5.5 years ago by • 0
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
1
vote
13
replies
14k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
7.6 years ago yjliu1127 • 0
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 ★ 13k • written 6.9 years ago by ▴ 10
3
votes
2
replies
296
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 10 weeks ago by ▴ 30 • written 10 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
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 65k • written 17 months ago by ▴ 10
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
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
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
3
votes
1
reply
1.7k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 30
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 41k • written 4.9 years ago by • 0
1
vote
1
reply
895
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
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
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
1
vote
2
replies
770
views
error loading kallisto output in tximport
file.exists false kallisto tximport
17 months ago cta • 0
0
votes
1
reply
668
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
801
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
11 months ago Yijing • 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
0
votes
0
replies
933
views
IsoformSwitchAnalyzeR error input
kallisto differential isoform usage isoform
6.5 years ago ilyco • 0
0
votes
4
replies
2.3k
views
Error in H5Fopen with kallisto .h5 files
tximport kallisto rhdf5
5.1 years ago uso2015 • 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
31 results • Page 1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
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…
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Install/Switch between multiple versions of R, Rstudio, and Bioconductor
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
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