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Views
Votes
Showing :
txImport
•
reset
0
votes
2
replies
139
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
16 days ago
Marianna
▴ 20
0
votes
2
replies
182
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 24 days ago by
Michael Love
41k • written 24 days ago by
SG
• 0
2
votes
1
reply
224
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
hemantcnaik
• 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 3 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
0
votes
1
reply
306
views
tximport error with rsem files
rsem
tximport
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
apolitics
• 0
3
votes
2
replies
539
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
mckinlee.salazar
• 0
0
votes
3
replies
400
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 5 months ago by
Abhishek
• 0 • written 6 months ago by
RLiu
▴ 40
2
votes
3
replies
785
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 8 months ago by
Vitor
• 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 months ago by
Michael Love
41k • written 7 months ago by
Christian
• 0
0
votes
4
replies
841
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 7 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 8 months ago by
k.vitting.seerup
▴ 120 • written 8 months ago by
elva.gypsophila
▴ 10
2
votes
9
replies
1.1k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
9 months ago
Ndimensional
▴ 20
0
votes
2
replies
632
views
tximport error in reading salmon output files?
tximport
tximportData
updated 11 weeks ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 0
0
votes
1
reply
586
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
629
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 11 months ago by
Michael Love
41k • written 11 months ago by
prangannathofficial
• 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
11 months ago
Yijing
• 0
0
votes
2
replies
802
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
11 months ago
Yijing
• 0
1
vote
3
replies
833
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
0
votes
2
replies
886
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
Ivana
• 0
1
vote
5
replies
1.1k
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
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 8 hours ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
701
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
766
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 15 months ago by
camilia.savitri
• 0
0
votes
1
reply
714
views
Missing transcript
DESeq2
tximport
salmon
updated 15 months ago by
ATpoint
★ 4.0k • written 15 months ago by
camilia.savitri
• 0
2
votes
1
reply
652
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 15 months ago by
ATpoint
★ 4.0k • written 15 months ago by
Dunois
• 0
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 8 weeks ago by
Michael Love
41k • written 16 months ago by
kiqbal
• 0
0
votes
2
replies
768
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
16 months ago
Konstantinos
• 0
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
16 months ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
1.0k
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
876
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 17 months ago by
ATpoint
★ 4.0k • written 17 months ago by
Jenni
• 0
1
vote
2
replies
771
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
17 months ago
cta
• 0
2
votes
2
replies
1.2k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
18 months ago
L
▴ 50
3
votes
3
replies
899
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 • updated 17 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
618
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
★ 4.0k • 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
★ 4.0k • written 19 months ago by
snowmattin
• 0
0
votes
3
replies
947
views
tximport error
error
tximport
updated 19 months ago by
Michael Love
41k • written 19 months ago by
hana
• 0
5
votes
6
replies
1.4k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2
limma
tximport
updated 19 months ago by
Gordon Smyth
50k • written 19 months ago by
Kent
• 0
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
21 months ago
uhlkatie
• 0
1
vote
3
replies
1.6k
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
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
22 months ago • updated 21 months ago
Kelen
▴ 10
0
votes
1
reply
986
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 23 months ago by
ATpoint
★ 4.0k • written 23 months ago by
johnmcma
▴ 10
0
votes
1
reply
834
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport
R
updated 23 months ago by
Michael Love
41k • written 23 months ago by
cthangav
• 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
23 months ago
Maka
• 0
5
votes
4
replies
2.2k
views
confused with tximport counts abundance using salmon input
RNASeq
tximport
2.0 years ago
Al90
▴ 10
0
votes
2
replies
2.4k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux
R
tximport
2.1 years ago
nakane_clan
• 0
2
votes
5
replies
1.7k
views
from kallisto to deseq2 analysis
biomaRt
DESeq2
tximport
2.2 years ago
Marianna
▴ 20
2
votes
3
replies
939
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
1 of 1
Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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