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Showing :
txImport
•
reset
0
votes
4
replies
1.1k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
9 days ago • updated 4 days ago
Sofia
• 0
0
votes
4
replies
523
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
4 weeks ago • updated 19 days ago
Nicholas
• 0
0
votes
11
replies
843
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 10 weeks ago by
Im
• 0 • written 11 weeks ago by
brown.annaleigh
• 0
1
vote
2
replies
694
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
3 months ago
georgii.vdovin
• 0
4
votes
5
replies
904
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
5 months ago
LuciaNhu
• 0
0
votes
2
replies
508
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 6 months ago by
Michael Love
43k • written 6 months ago by
oguzhankaraosmanoglu
• 0
0
votes
2
replies
501
views
tximport data import
tximport
updated 7 months ago by
Michael Love
43k • written 7 months ago by
rodongo
• 0
1
vote
2
replies
975
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
8 months ago
grothmn
• 0
1
vote
2
replies
2.4k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 10 months ago by
rodrigo.duarte88
▴ 40 • written 5.4 years ago by
mohamedrefaat.1.1992
• 0
0
votes
4
replies
727
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
10 months ago
JG13
• 0
0
votes
2
replies
680
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
12 months ago
Marianna
▴ 20
0
votes
2
replies
732
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 12 months ago by
Michael Love
43k • written 12 months ago by
SG
• 0
2
votes
1
reply
628
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 12 months ago by
ATpoint
★ 4.8k • written 12 months ago by
hemantcnaik
• 0
2
votes
3
replies
2.9k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 15 months ago by
swbarnes2
★ 1.4k • written 16 months ago by
Bo
• 0
0
votes
1
reply
850
views
tximport error with rsem files
rsem
tximport
updated 15 months ago by
ATpoint
★ 4.8k • written 15 months ago by
apolitics
• 0
3
votes
2
replies
1.1k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
mckinlee.salazar
• 0
0
votes
3
replies
978
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 17 months ago by
Michael Love
43k • written 17 months ago by
Kayleigh
• 0
10
votes
11
replies
3.0k
views
tximport error: vroom
tximport
updated 17 months ago by
Abhishek
• 0 • written 18 months ago by
RLiu
▴ 40
2
votes
3
replies
1.3k
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 19 months ago by
Vitor
• 0
5
votes
13
replies
3.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 18 months ago by
Michael Love
43k • written 19 months ago by
Christian
• 0
2
votes
4
replies
1.7k
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 19 months ago by
Michael Love
43k • written 19 months ago by
hanc
▴ 10
1
vote
2
replies
2.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 20 months ago by
k.vitting.seerup
▴ 120 • written 20 months ago by
elva.gypsophila
▴ 10
2
votes
9
replies
1.9k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
21 months ago
Ndimensional
▴ 20
0
votes
2
replies
1.0k
views
tximport error in reading salmon output files?
tximport
tximportData
updated 14 months ago by
Matteo
• 0 • written 21 months ago by
barrypraveen
• 0
0
votes
1
reply
989
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Yijing
• 0
2
votes
1
reply
1.2k
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 23 months ago by
Michael Love
43k • written 23 months ago by
prangannathofficial
• 0
3
votes
7
replies
1.7k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
23 months ago
Yijing
• 0
0
votes
2
replies
1.4k
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
23 months ago
Yijing
• 0
1
vote
3
replies
1.4k
views
tximport error
tximport
r
updated 23 months ago by
Michael Love
43k • written 23 months ago by
Joana
• 0
0
votes
2
replies
1.5k
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 2.1 years ago by
ATpoint
★ 4.8k • written 2.1 years ago by
Ivana
• 0
1
vote
5
replies
1.8k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Michael Steinbaugh
▴ 90
6
votes
10
replies
3.3k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 11 months ago by
i.atanasoai
• 0 • written 2.2 years ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.1k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 2.2 years ago by
Dario Strbenac
★ 1.6k • written 2.2 years ago by
Hicham
▴ 10
0
votes
2
replies
1.4k
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 2.2 years ago by
camilia.savitri
• 0
0
votes
1
reply
1.2k
views
Missing transcript
DESeq2
tximport
salmon
updated 2.2 years ago by
ATpoint
★ 4.8k • written 2.2 years ago by
camilia.savitri
• 0
2
votes
5
replies
2.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 13 months ago by
Michael Love
43k • written 2.3 years ago by
kiqbal
• 0
0
votes
2
replies
1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
2.3 years ago
Konstantinos
• 0
2
votes
3
replies
1.8k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
2.3 years ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
1.6k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Mikhail Biryukov
▴ 10
0
votes
1
reply
1.3k
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 2.4 years ago by
ATpoint
★ 4.8k • written 2.4 years ago by
Jenni
• 0
1
vote
2
replies
1.2k
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
2.4 years ago
cta
• 0
2
votes
3
replies
2.0k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
written 2.5 years ago by
L
▴ 50
3
votes
3
replies
1.5k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
2.5 years ago • updated 2.4 years ago
duhwa.lee
• 0
1
vote
2
replies
2.3k
views
transcripts missing from tx2gene
tximport
2.5 years ago
Erick
• 0
0
votes
1
reply
969
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
凯
• 0
3
votes
1
reply
3.2k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 2.6 years ago by
ATpoint
★ 4.8k • written 2.6 years ago by
Florent
▴ 10
3
votes
4
replies
2.1k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq
tximport
updated 2.6 years ago by
ATpoint
★ 4.8k • written 2.6 years ago by
snowmattin
• 0
0
votes
3
replies
1.4k
views
tximport error
error
tximport
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
hana
• 0
5
votes
6
replies
2.2k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2
limma
tximport
updated 2.6 years ago by
Gordon Smyth
52k • written 2.6 years ago by
Kent
• 0
0
votes
4
replies
1.6k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
2.8 years ago
uhlkatie
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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