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tximport
•
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0
votes
1
reply
199
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 7 days ago by
ATpoint
★ 4.8k • written 8 days ago by
yob4003
• 0
0
votes
4
replies
1.2k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
7 weeks ago • updated 6 weeks ago
Sofia
• 0
0
votes
4
replies
610
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
10 weeks ago • updated 9 weeks ago
Nicholas
• 0
0
votes
11
replies
961
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 3 months ago by
Im
• 0 • written 4 months ago by
brown.annaleigh
• 0
1
vote
2
replies
866
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
5 months ago
georgii.vdovin
• 0
4
votes
5
replies
1.0k
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
6 months ago
LuciaNhu
• 0
0
votes
2
replies
555
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 7 months ago by
Michael Love
43k • written 7 months ago by
oguzhankaraosmanoglu
• 0
0
votes
2
replies
537
views
tximport data import
tximport
updated 8 months ago by
Michael Love
43k • written 8 months ago by
rodongo
• 0
1
vote
2
replies
1.1k
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
9 months ago
grothmn
• 0
1
vote
2
replies
2.5k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 11 months ago by
rodrigo.duarte88
▴ 40 • written 5.6 years ago by
mohamedrefaat.1.1992
• 0
0
votes
4
replies
765
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
11 months ago
JG13
• 0
0
votes
2
replies
727
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
13 months ago
Marianna
▴ 20
0
votes
2
replies
809
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 13 months ago by
Michael Love
43k • written 13 months ago by
SG
• 0
2
votes
1
reply
665
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 14 months ago by
ATpoint
★ 4.8k • written 14 months ago by
hemantcnaik
• 0
2
votes
3
replies
3.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 17 months ago by
swbarnes2
★ 1.4k • written 17 months ago by
Bo
• 0
0
votes
1
reply
887
views
tximport error with rsem files
rsem
tximport
updated 17 months ago by
ATpoint
★ 4.8k • written 17 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 17 months ago by
James W. MacDonald
68k • written 17 months ago by
mckinlee.salazar
• 0
0
votes
3
replies
1.0k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
Kayleigh
• 0
10
votes
11
replies
3.2k
views
tximport error: vroom
tximport
updated 19 months ago by
Abhishek
• 0 • written 19 months ago by
RLiu
▴ 40
2
votes
3
replies
1.4k
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 21 months ago by
Vitor
• 0
5
votes
13
replies
3.7k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 20 months ago by
Michael Love
43k • written 20 months ago by
Christian
• 0
2
votes
4
replies
1.8k
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 20 months ago by
Michael Love
43k • written 21 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 21 months ago by
k.vitting.seerup
▴ 120 • written 22 months ago by
elva.gypsophila
▴ 10
2
votes
9
replies
2.0k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
22 months ago
Ndimensional
▴ 20
0
votes
2
replies
1.1k
views
tximport error in reading salmon output files?
tximport
tximportData
updated 15 months ago by
Matteo
• 0 • written 23 months ago by
barrypraveen
• 0
0
votes
1
reply
1.0k
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
Yijing
• 0
2
votes
1
reply
1.2k
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
prangannathofficial
• 0
3
votes
7
replies
1.7k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
2.0 years ago
Yijing
• 0
0
votes
2
replies
1.4k
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
2.1 years ago • updated 2.0 years ago
Yijing
• 0
1
vote
3
replies
1.5k
views
tximport error
tximport
r
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Joana
• 0
0
votes
2
replies
1.6k
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 2.2 years ago by
ATpoint
★ 4.8k • written 2.3 years ago by
Ivana
• 0
1
vote
5
replies
1.8k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
Michael Steinbaugh
▴ 90
6
votes
10
replies
3.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 months ago by
i.atanasoai
• 0 • written 2.3 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 2.3 years ago by
Dario Strbenac
★ 1.6k • written 2.3 years ago by
Hicham
▴ 10
0
votes
2
replies
1.4k
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 2.4 years ago by
camilia.savitri
• 0
0
votes
1
reply
1.2k
views
Missing transcript
DESeq2
tximport
salmon
updated 2.4 years ago by
ATpoint
★ 4.8k • written 2.4 years ago by
camilia.savitri
• 0
2
votes
5
replies
2.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 15 months ago by
Michael Love
43k • written 2.4 years ago by
kiqbal
• 0
0
votes
2
replies
1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
2.5 years ago
Konstantinos
• 0
2
votes
3
replies
1.9k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
2.5 years ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
1.7k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 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 2.5 years ago by
ATpoint
★ 4.8k • written 2.5 years ago by
Jenni
• 0
1
vote
2
replies
1.2k
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
2.5 years ago
cta
• 0
2
votes
3
replies
2.3k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
updated 26 days ago by
ben
• 0 • written 2.6 years ago by
L
▴ 50
3
votes
3
replies
1.6k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
2.6 years ago • updated 2.5 years ago
duhwa.lee
• 0
1
vote
2
replies
2.4k
views
transcripts missing from tx2gene
tximport
2.7 years ago
Erick
• 0
0
votes
1
reply
997
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
凯
• 0
3
votes
1
reply
3.5k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 2.7 years ago by
ATpoint
★ 4.8k • written 2.7 years ago by
Florent
▴ 10
3
votes
4
replies
2.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq
tximport
updated 2.7 years ago by
ATpoint
★ 4.8k • written 2.7 years ago by
snowmattin
• 0
0
votes
3
replies
1.4k
views
tximport error
error
tximport
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
hana
• 0
5
votes
6
replies
2.3k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2
limma
tximport
updated 2.7 years ago by
Gordon Smyth
52k • written 2.7 years ago by
Kent
• 0
50 results • Page
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Replies
Answer: Limma suqeezeVar
by
Gordon Smyth
52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
Comment: Discrepancies in normalised count data vs unnormalised
by
swbarnes2
★ 1.4k
Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…
Comment: Can't install BioC packages (and manager) behind firewall
by
Marcel Ramos
700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa
by
Alejandro
• 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error
by
asafpr
• 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Votes
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
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