Showing : kallisto • reset
3
votes
7
replies
553
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
4 months ago Yijing • 0
0
votes
2
replies
357
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
4 months ago Yijing • 0
4
votes
3
replies
605
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 10 months ago by 63k • written 10 months ago by ▴ 10
1
vote
2
replies
476
views
error loading kallisto output in tximport
file.exists false kallisto tximport
10 months ago cta • 0
3
votes
3
replies
548
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
11 months ago • updated 10 months ago duhwa.lee • 0
2
votes
1
reply
1.2k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 23 months ago by 40k • written 23 months ago by • 0
0
votes
1
reply
511
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
0
votes
2
replies
2.5k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 2.9 years ago by 40k • written 2.9 years ago by • 0
1
vote
9
replies
2.4k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 3.4 years ago by 40k • written 3.4 years ago by • 0
0
votes
2
replies
1.2k
views
error in creating kallisto index
kallisto
updated 3.4 years ago by 40k • written 3.4 years ago by ▴ 20
2
votes
4
replies
3.7k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
4.4 years ago • updated 3.5 years ago Mozart ▴ 20
1
vote
1
reply
692
views
tximport errors with h5 and tsv files
tximport kallisto
updated 3.8 years ago by 40k • written 3.8 years ago by • 0
0
votes
6
replies
1.1k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 4.3 years ago by 40k • written 4.3 years ago by • 0
3
votes
1
reply
1.4k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 4.4 years ago by 40k • written 4.4 years ago by ▴ 20
0
votes
4
replies
2.0k
views
Error in H5Fopen with kallisto .h5 files
tximport kallisto rhdf5
4.5 years ago uso2015 • 0
1
vote
5
replies
2.5k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 4.7 years ago by 40k • written 4.7 years ago by • 0
2
votes
3
replies
1.3k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport kallisto
updated 4.7 years ago by 48k • written 4.7 years ago by ▴ 40
6
votes
6
replies
1.9k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 5.0 years ago by ★ 1.9k • written 5.0 years ago by • 0
1
vote
4
replies
2.2k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 5.5 years ago by 40k • written 5.5 years ago by • 0
0
votes
1
reply
905
views
Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
5.7 years ago srdjan.kasapovic0 • 0
2
votes
4
replies
2.0k
views
tximport of kallisto files
tximport deseq2 kallisto
updated 5.8 years ago by 40k • written 5.8 years ago by • 0
0
votes
0
replies
775
views
IsoformSwitchAnalyzeR error input
kallisto differential isoform usage isoform
5.9 years ago ilyco • 0
3
votes
3
replies
1.2k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 6.0 years ago by 40k • written 6.0 years ago by ▴ 20
0
votes
1
reply
1.0k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2 kallisto
updated 6.0 years ago by 40k • written 6.0 years ago by ▴ 20
2
votes
2
replies
1.8k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport kallisto txdb.mmusculus.ucsc.mm10.knowngene
updated 6.3 years ago by 63k • written 6.3 years ago by • 0
0
votes
3
replies
1.8k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 6.3 years ago by 40k • written 6.3 years ago by • 0
0
votes
7
replies
2.2k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 22 months ago by • 0 • written 6.3 years ago by ▴ 40
2
votes
5
replies
3.2k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 6.4 years ago by 13k • written 6.4 years ago by ▴ 10
9
votes
11
replies
5.2k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 6.6 years ago by ▴ 20 • written 7.4 years ago by ▴ 10
1
vote
13
replies
12k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
7.1 years ago • updated 7.0 years ago yjliu1127 • 0
30 results • Page 1 of 1
Recent ...
Replies
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Comment: DMRcate design by James W. MacDonald 63k
That's what identical context means.
Votes
Comment: Speeding up of DelayedArray::write_block()
Answer: DelayedArray::read_sparse_block
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
Awards • All
Popular Question to Hervé Pagès 16k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to sohail.mbio ▴ 10
Popular Question to komal.rathi ▴ 110
Popular Question to Levi Waldron 1.1k
Locations • All
Japan, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Canada, 1 hour ago
United States, 3 hours ago
Seattle, WA, United States, 3 hours ago
Traffic: 372 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6