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Showing :
tximport
•
reset
0
votes
4
replies
495
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
16 days ago • updated 5 days ago
Nicholas
• 0
0
votes
11
replies
808
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 8 weeks ago by
Im
• 0 • written 9 weeks ago by
brown.annaleigh
• 0
1
vote
2
replies
657
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
3 months ago
georgii.vdovin
• 0
4
votes
5
replies
871
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
4 months ago
LuciaNhu
• 0
0
votes
2
replies
490
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
oguzhankaraosmanoglu
• 0
0
votes
2
replies
498
views
tximport data import
tximport
updated 6 months ago by
Michael Love
43k • written 6 months ago by
rodongo
• 0
1
vote
2
replies
946
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
7 months ago
grothmn
• 0
1
vote
2
replies
2.4k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 9 months ago by
rodrigo.duarte88
▴ 40 • written 5.4 years ago by
mohamedrefaat.1.1992
• 0
0
votes
4
replies
708
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
9 months ago
JG13
• 0
0
votes
2
replies
665
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
11 months ago
Marianna
▴ 20
0
votes
2
replies
713
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
611
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 12 months ago by
ATpoint
★ 4.7k • 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 15 months ago by
Bo
• 0
0
votes
1
reply
837
views
tximport error with rsem files
rsem
tximport
updated 15 months ago by
ATpoint
★ 4.7k • 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
965
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 17 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
3.2k
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
20 months ago
Ndimensional
▴ 20
0
votes
2
replies
1.0k
views
tximport error in reading salmon output files?
tximport
tximportData
updated 13 months ago by
Matteo
• 0 • written 21 months ago by
barrypraveen
• 0
0
votes
1
reply
978
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Yijing
• 0
2
votes
1
reply
1.2k
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 22 months ago by
Michael Love
43k • written 22 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 • updated 22 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
★ 4.7k • 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
3.2k
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 2.1 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
1.3k
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
★ 4.7k • written 2.2 years ago by
camilia.savitri
• 0
2
votes
1
reply
1.1k
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 2.2 years ago by
ATpoint
★ 4.7k • written 2.2 years ago by
Dunois
• 0
2
votes
5
replies
2.2k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 13 months ago by
Michael Love
43k • written 2.2 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 2.3 years ago by
James W. MacDonald
68k • written 2.3 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 2.3 years ago by
ATpoint
★ 4.7k • written 2.3 years ago by
Jenni
• 0
1
vote
2
replies
1.1k
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
2.4 years ago
cta
• 0
2
votes
3
replies
1.9k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
written 2.4 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
2.4 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
962
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
3.1k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 2.5 years ago by
ATpoint
★ 4.7k • written 2.5 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 2.5 years ago by
ATpoint
★ 4.7k • written 2.5 years ago by
snowmattin
• 0
0
votes
3
replies
1.3k
views
tximport error
error
tximport
updated 2.5 years ago by
Michael Love
43k • written 2.5 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 2.5 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
2.7 years ago
uhlkatie
• 0
50 results • Page
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Recent ...
Replies
Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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