Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
txImport
•
reset
0
votes
2
replies
142
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
17 days ago • updated 16 days ago
Marianna
▴ 20
0
votes
2
replies
185
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 24 days ago by
Michael Love
41k • written 25 days ago by
SG
• 0
2
votes
1
reply
225
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
309
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
540
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
402
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
786
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
634
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
588
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
631
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
803
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
11 months ago
Yijing
• 0
1
vote
3
replies
836
views
tximport error
tximport
r
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Joana
• 0
0
votes
2
replies
889
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 1 day ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
704
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
768
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 15 months ago by
camilia.savitri
• 0
0
votes
1
reply
718
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
657
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
879
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
902
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
948
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
988
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
835
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
2.2 years ago • updated 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
941
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: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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
Awards
• All
Scholar
to
Robert Castelo
★ 3.2k
Popular Question
to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Popular Question
to
BioinfGuru
▴ 30
Popular Question
to
Gordon Smyth
50k
Locations
• All
France,
9 minutes ago
Italy,
10 minutes ago
Ireland,
20 minutes ago
Ghana,
38 minutes ago
WEHI, Melbourne, Australia,
59 minutes ago
Traffic: 458 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6