Showing : Kallisto • reset
4
votes
2
replies
1.6k
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 10 months ago by ▴ 40 • written 10 months ago by • 0
3
votes
7
replies
1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
20 months ago Yijing • 0
0
votes
2
replies
1.2k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
20 months ago Yijing • 0
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 10
1
vote
2
replies
1.1k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.1 years ago cta • 0
3
votes
3
replies
1.4k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.2 years ago duhwa.lee • 0
2
votes
1
reply
2.1k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
1
reply
862
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 3.5 years ago by 67k • written 3.5 years ago by • 0
0
votes
2
replies
3.6k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
1
vote
9
replies
3.4k
views
Importing Kallisto counts with tximport
tximport Kallisto H5Fopen
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
2
replies
2.0k
views
error in creating kallisto index
kallisto
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
2
votes
4
replies
5.5k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto tximport deseq2 counts
5.7 years ago • updated 4.8 years ago Mozart ▴ 30
1
vote
1
reply
1.1k
views
tximport errors with h5 and tsv files
tximport kallisto
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
6
replies
1.7k
views
how to set offset matrix to Deseq2 differential analysis
deseq2 Kallisto tximport
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
3
votes
1
reply
2.1k
views
Tximport and pseudo alignment with Kallisto
kallisto tximport deseq2
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 30
0
votes
4
replies
2.8k
views
Error in H5Fopen with kallisto .h5 files
tximport kallisto rhdf5
5.8 years ago uso2015 • 0
1
vote
5
replies
3.3k
views
tximport error with kallisto .h5 files
deseq2 kallisto tximport
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
3
replies
1.8k
views
tximport: kallisto .h5 files not recognized as such when they have a different name
tximport kallisto
updated 6.0 years ago by 52k • written 6.0 years ago by ▴ 40
6
votes
6
replies
2.7k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 6.2 years ago by ★ 1.9k • written 6.2 years ago by • 0
1
vote
4
replies
2.9k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
votes
1
reply
1.2k
views
Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
7.0 years ago srdjan.kasapovic0 • 0
2
votes
4
replies
2.8k
views
tximport of kallisto files
tximport deseq2 kallisto
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
votes
0
replies
1.1k
views
IsoformSwitchAnalyzeR error input
kallisto differential isoform usage isoform
7.2 years ago ilyco • 0
3
votes
3
replies
1.6k
views
Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
0
votes
1
reply
1.6k
views
Importing kallisto's abundance files into DESeq2 pipeline
deseq2 kallisto
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
2
votes
2
replies
2.1k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport kallisto txdb.mmusculus.ucsc.mm10.knowngene
updated 7.6 years ago by 67k • written 7.6 years ago by • 0
0
votes
3
replies
2.2k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
7
replies
2.7k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 3.2 years ago by • 0 • written 7.6 years ago by ▴ 40
2
votes
5
replies
3.9k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 7.6 years ago by ★ 13k • written 7.6 years ago by ▴ 10
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.8 years ago by ▴ 20 • written 8.7 years ago by ▴ 10
1
vote
13
replies
15k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
8.3 years ago yjliu1127 • 0
31 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to rohitsatyam102 ▴ 20
Popular Question to Hervé Pagès 16k
Teacher to dsull ▴ 40
Locations • All
Sweden, 13 minutes ago
India, 29 minutes ago
United States, 1 hour ago
Sweden, 4 hours ago
UPF, Barcelona, Spain, 4 hours ago
Traffic: 620 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