Showing : Kallisto • reset
0
votes
3
replies
973
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 5 months ago by • 0 • written 5 months ago by • 0
0
votes
4
replies
869
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
9 months ago • updated 8 months ago Nicholas • 0
4
votes
2
replies
2.7k
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 22 months ago by ▴ 40 • written 22 months ago by • 0
3
votes
7
replies
2.0k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.6 years ago Yijing • 0
0
votes
2
replies
1.7k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.6 years ago Yijing • 0
4
votes
3
replies
1.9k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 10
1
vote
2
replies
1.4k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
3.1 years ago cta • 0
3
votes
3
replies
1.8k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
3.1 years ago duhwa.lee • 0
2
votes
1
reply
2.6k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
votes
1
reply
1.1k
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
votes
2
replies
4.3k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
1
vote
9
replies
4.1k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
0
votes
2
replies
2.3k
views
error in creating kallisto index
kallisto
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 20
2
votes
4
replies
6.5k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
6.6 years ago • updated 5.7 years ago Mozart ▴ 30
1
vote
1
reply
1.3k
views
tximport errors with h5 and tsv files
tximport kallisto
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
6
replies
2.1k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
3
votes
1
reply
2.4k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 30
0
votes
4
replies
3.4k
views
Error in H5Fopen with kallisto .h5 files
tximport kallisto rhdf5
6.7 years ago uso2015 • 0
1
vote
5
replies
3.7k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
3
replies
2.1k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport kallisto
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 40
6
votes
6
replies
3.2k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 7.2 years ago by ★ 1.9k • written 7.2 years ago by • 0
1
vote
4
replies
3.2k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
votes
1
reply
1.4k
views
Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
7.9 years ago srdjan.kasapovic0 • 0
2
votes
4
replies
3.2k
views
tximport of kallisto files
tximport deseq2 kallisto
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
votes
0
replies
1.3k
views
IsoformSwitchAnalyzeR error input
kallisto differential isoform usage isoform
8.1 years ago ilyco • 0
3
votes
3
replies
1.9k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
votes
1
reply
1.8k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2 kallisto
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
2
votes
2
replies
2.5k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport kallisto txdb.mmusculus.ucsc.mm10.knowngene
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
votes
3
replies
2.5k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
0
votes
7
replies
3.1k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 4.1 years ago by • 0 • written 8.5 years ago by ▴ 40
2
votes
5
replies
4.3k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 8.6 years ago by ★ 13k • written 8.6 years ago by ▴ 10
9
votes
11
replies
6.3k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.8 years ago by ▴ 20 • written 9.6 years ago by ▴ 10
1
vote
13
replies
16k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
9.3 years ago • updated 9.2 years ago yjliu1127 • 0
33 results • Page 1 of 1
Recent ...
Replies
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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