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Votes
Showing :
Tximport
•
reset
0
votes
2
replies
168
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
4 weeks ago
Marianna
▴ 20
0
votes
2
replies
208
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
SG
• 0
2
votes
1
reply
248
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 7 weeks ago by
ATpoint
★ 4.1k • written 7 weeks ago by
hemantcnaik
• 0
0
votes
1
reply
353
views
tximport error with rsem files
rsem
tximport
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
apolitics
• 0
2
votes
3
replies
1.2k
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
★ 1.3k • written 4 months ago by
Bo
• 0
3
votes
2
replies
562
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
429
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
Kayleigh
• 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by
Abhishek
• 0 • written 7 months ago by
RLiu
▴ 40
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 7 months ago by
Michael Love
41k • written 8 months ago by
Christian
• 0
0
votes
4
replies
885
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 8 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
2
votes
3
replies
814
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 8 months ago by
Vitor
• 0
1
vote
2
replies
1.5k
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
665
views
tximport error in reading salmon output files?
tximport
tximportData
updated 3 months ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
0
votes
1
reply
615
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Yijing
• 0
2
votes
1
reply
656
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 12 months ago by
Michael Love
41k • 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
826
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
12 months ago
Yijing
• 0
1
vote
3
replies
871
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
0
votes
2
replies
922
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
Ivana
• 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 14 months ago by
Michael Love
41k • written 14 months ago by
Michael Steinbaugh
▴ 90
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 16 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
730
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 15 months ago by
Dario Strbenac
★ 1.5k • written 15 months ago by
Hicham
▴ 10
0
votes
2
replies
802
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 16 months ago by
camilia.savitri
• 0
0
votes
1
reply
742
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
687
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 10 weeks ago by
Michael Love
41k • written 16 months ago by
kiqbal
• 0
0
votes
2
replies
785
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 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Mikhail Biryukov
▴ 10
0
votes
1
reply
897
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 17 months ago by
ATpoint
★ 4.1k • written 17 months ago by
Jenni
• 0
1
vote
2
replies
797
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
18 months ago
L
▴ 50
3
votes
3
replies
936
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
18 months ago
duhwa.lee
• 0
1
vote
2
replies
1.5k
views
transcripts missing from tx2gene
tximport
19 months ago
Erick
• 0
0
votes
1
reply
632
views
tximport: not all(file.exists(files)) are true
tximport
updated 19 months ago by
Michael Love
41k • written 19 months ago by
凯
• 0
2
votes
1
reply
1.5k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 19 months ago by
ATpoint
★ 4.1k • written 19 months ago by
Florent
▴ 10
3
votes
4
replies
1.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq
tximport
updated 19 months ago by
ATpoint
★ 4.1k • written 20 months ago by
snowmattin
• 0
0
votes
3
replies
978
views
tximport error
error
tximport
updated 20 months ago by
Michael Love
41k • 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
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
22 months ago
Kelen
▴ 10
1
vote
3
replies
1.7k
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 22 months ago by
Michael Love
41k • written 22 months ago by
BG
• 0
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
johnmcma
▴ 10
0
votes
1
reply
851
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport
R
updated 24 months ago by
Michael Love
41k • 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
5
votes
4
replies
2.3k
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
2.2 years ago
Marianna
▴ 20
2
votes
3
replies
960
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Luisa
• 0
50 results • Page
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I don't follow your point. limma's camera method has been formally cited in nea…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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