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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
James W. MacDonald
63k • written 10 months ago by
Mikhail Biryukov
▴ 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
Michael Love
40k • written 23 months ago by
BioNovice247
• 0
0
votes
1
reply
511
views
Pseudoalignment for repetitive sequences
Kallisto
RNASeq
pseudoaligners
ShortTandemRepeats
updated 2.2 years ago by
James W. MacDonald
63k • written 2.2 years ago by
Shu Yi
• 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
Michael Love
40k • written 2.9 years ago by
m93
• 0
1
vote
9
replies
2.4k
views
Importing Kallisto counts with tximport
tximport
Kallisto
H5Fopen
updated 3.4 years ago by
Michael Love
40k • written 3.4 years ago by
zroger499
• 0
0
votes
2
replies
1.2k
views
error in creating kallisto index
kallisto
updated 3.4 years ago by
Michael Love
40k • written 3.4 years ago by
biok0423
▴ 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
Michael Love
40k • written 3.8 years ago by
sp21
• 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
Michael Love
40k • written 4.3 years ago by
qwzhang0601
• 0
3
votes
1
reply
1.4k
views
Tximport and pseudo alignment with Kallisto
kallisto
tximport
deseq2
updated 4.4 years ago by
Michael Love
40k • written 4.4 years ago by
Mozart
▴ 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
Michael Love
40k • written 4.7 years ago by
steve.standage
• 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
Gordon Smyth
48k • written 4.7 years ago by
Lucas Carey
▴ 40
6
votes
6
replies
1.9k
views
Kallisto output with DEXSeq
dexseq
kallisto
NH_tag
updated 5.0 years ago by
Alejandro Reyes
★ 1.9k • written 5.0 years ago by
j2h2k2
• 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
Michael Love
40k • written 5.5 years ago by
Yunlu Zhu
• 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
Michael Love
40k • written 5.8 years ago by
Clara
• 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
Michael Love
40k • written 6.0 years ago by
thibault.lorin34
▴ 20
0
votes
1
reply
1.0k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2
kallisto
updated 6.0 years ago by
Michael Love
40k • written 6.0 years ago by
deena
▴ 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
James W. MacDonald
63k • written 6.3 years ago by
Kaustav
• 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
Michael Love
40k • written 6.3 years ago by
birgittenilsson
• 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
nicolette.sipperly
• 0 • written 6.3 years ago by
urjaswita
▴ 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
Steve Lianoglou
13k • written 6.4 years ago by
swamyvinny
▴ 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
pablo_garcia05
▴ 20 • written 7.4 years ago by
cguzman.bioinformatics
▴ 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
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