Showing : kallisto • reset
0
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3
replies
994
views
Many transcripts missing from tx2gene created from Ensembl GTF file
kallisto tximport ensembl
updated 5 months ago by • 0 • written 6 months ago by • 0
0
votes
4
replies
886
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
9 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
2.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
2.6 years ago Yijing • 0
0
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2
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1.7k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
2.6 years ago Yijing • 0
4
votes
3
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1.9k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 10
1
vote
2
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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
3.2 years ago • updated 3.1 years ago duhwa.lee • 0
2
votes
1
reply
2.7k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 4.2 years ago by 43k • written 4.2 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 5.7 years ago by 43k • written 5.7 years ago by • 0
0
votes
2
replies
2.4k
views
error in creating kallisto index
kallisto
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 20
2
votes
4
replies
6.6k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
6.7 years ago • updated 5.7 years ago Mozart ▴ 30
1
vote
1
reply
1.4k
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
2.5k
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 7.0 years ago by 53k • written 7.0 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 7.8 years ago by 43k • written 7.8 years ago by • 0
0
votes
1
reply
1.5k
views
Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
8.0 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 8.3 years ago by 43k • written 8.3 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 8.6 years ago by ▴ 40
2
votes
5
replies
4.4k
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
6.4k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.8 years ago by ▴ 20 • written 9.7 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 yjliu1127 • 0
33 results • Page 1 of 1
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
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
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