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Views
Votes
Showing :
tximport
•
reset
0
votes
2
replies
198
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
6 weeks ago
Marianna
▴ 20
0
votes
2
replies
216
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 7 weeks ago by
Michael Love
42k • written 7 weeks ago by
SG
• 0
2
votes
1
reply
272
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 9 weeks ago by
ATpoint
★ 4.1k • written 9 weeks ago by
hemantcnaik
• 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
Bo
• 0
0
votes
1
reply
368
views
tximport error with rsem files
rsem
tximport
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
apolitics
• 0
3
votes
2
replies
586
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
mckinlee.salazar
• 0
0
votes
3
replies
452
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
Kayleigh
• 0
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 7 months ago by
RLiu
▴ 40
2
votes
3
replies
842
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 9 months ago by
Vitor
• 0
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 months ago by
Michael Love
42k • written 8 months ago by
Christian
• 0
0
votes
4
replies
921
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 8 months ago by
Michael Love
42k • written 9 months ago by
hanc
• 0
1
vote
2
replies
1.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 9 months ago by
k.vitting.seerup
▴ 120 • written 9 months ago by
elva.gypsophila
▴ 10
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
0
votes
2
replies
685
views
tximport error in reading salmon output files?
tximport
tximportData
updated 3 months ago by
Matteo
• 0 • written 11 months ago by
barrypraveen
• 0
0
votes
1
reply
641
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
Yijing
• 0
2
votes
1
reply
677
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 12 months ago by
Michael Love
42k • written 12 months ago by
prangannathofficial
• 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
12 months ago
Yijing
• 0
0
votes
2
replies
851
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
12 months ago
Yijing
• 0
1
vote
3
replies
890
views
tximport error
tximport
r
updated 13 months ago by
Michael Love
42k • written 13 months ago by
Joana
• 0
0
votes
2
replies
946
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 15 months ago by
ATpoint
★ 4.1k • written 15 months ago by
Ivana
• 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 15 months ago by
Michael Love
42k • written 15 months ago by
Michael Steinbaugh
▴ 90
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
751
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 16 months ago by
Dario Strbenac
★ 1.5k • written 16 months ago by
Hicham
▴ 10
0
votes
2
replies
824
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 16 months ago by
camilia.savitri
• 0
0
votes
1
reply
767
views
Missing transcript
DESeq2
tximport
salmon
updated 16 months ago by
ATpoint
★ 4.1k • written 16 months ago by
camilia.savitri
• 0
2
votes
1
reply
707
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 16 months ago by
ATpoint
★ 4.1k • written 16 months ago by
Dunois
• 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 12 weeks ago by
Michael Love
42k • written 17 months ago by
kiqbal
• 0
0
votes
2
replies
802
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
17 months ago
Konstantinos
• 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
17 months ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
1.1k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Mikhail Biryukov
▴ 10
0
votes
1
reply
914
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 18 months ago by
ATpoint
★ 4.1k • written 18 months ago by
Jenni
• 0
1
vote
2
replies
811
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
18 months ago
cta
• 0
2
votes
2
replies
1.3k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
19 months ago
L
▴ 50
3
votes
3
replies
961
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
19 months ago • updated 18 months ago
duhwa.lee
• 0
1
vote
2
replies
1.6k
views
transcripts missing from tx2gene
tximport
20 months ago
Erick
• 0
0
votes
1
reply
649
views
tximport: not all(file.exists(files)) are true
tximport
updated 20 months ago by
Michael Love
42k • written 20 months ago by
凯
• 0
2
votes
1
reply
1.6k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
Florent
▴ 10
3
votes
4
replies
1.3k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq
tximport
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
snowmattin
• 0
0
votes
3
replies
993
views
tximport error
error
tximport
updated 20 months ago by
Michael Love
42k • written 20 months ago by
hana
• 0
5
votes
6
replies
1.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2
limma
tximport
updated 20 months ago by
Gordon Smyth
50k • written 20 months ago by
Kent
• 0
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
22 months ago
uhlkatie
• 0
1
vote
3
replies
1.7k
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 23 months ago by
Michael Love
42k • written 23 months ago by
BG
• 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
23 months ago • updated 22 months ago
Kelen
▴ 10
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 2.0 years ago by
ATpoint
★ 4.1k • written 2.0 years ago by
johnmcma
▴ 10
0
votes
1
reply
863
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport
R
updated 2.0 years ago by
Michael Love
42k • written 2.0 years ago by
cthangav
• 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
2.0 years ago
Maka
• 0
6
votes
4
replies
2.4k
views
confused with tximport counts abundance using salmon input
RNASeq
tximport
2.1 years ago
Al90
▴ 10
0
votes
2
replies
2.5k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux
R
tximport
2.2 years ago
nakane_clan
• 0
2
votes
5
replies
1.8k
views
from kallisto to deseq2 analysis
biomaRt
DESeq2
tximport
2.3 years ago
Marianna
▴ 20
2
votes
3
replies
973
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Luisa
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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