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
1
vote
2
replies
470
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
4 weeks ago
georgii.vdovin
• 0
4
votes
5
replies
672
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
10 weeks ago • updated 9 weeks ago
LuciaNhu
• 0
0
votes
2
replies
406
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
oguzhankaraosmanoglu
• 0
0
votes
2
replies
439
views
tximport data import
tximport
updated 4 months ago by
Michael Love
43k • written 4 months ago by
rodongo
• 0
1
vote
2
replies
820
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
5 months ago
grothmn
• 0
1
vote
2
replies
2.3k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 7 months ago by
rodrigo.duarte88
▴ 40 • written 5.2 years ago by
mohamedrefaat.1.1992
• 0
0
votes
4
replies
623
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
7 months ago
JG13
• 0
0
votes
2
replies
576
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
9 months ago
Marianna
▴ 20
0
votes
2
replies
613
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 9 months ago by
Michael Love
43k • written 9 months ago by
SG
• 0
2
votes
1
reply
527
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 10 months ago by
ATpoint
★ 4.6k • written 10 months ago by
hemantcnaik
• 0
0
votes
2
replies
947
views
tximport error in reading salmon output files?
tximport
tximportData
updated 11 months ago by
Matteo
• 0 • written 19 months ago by
barrypraveen
• 0
6
votes
10
replies
2.8k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 8 months ago by
i.atanasoai
• 0 • written 23 months ago by
mohammedtoufiq91
▴ 10
2
votes
5
replies
2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 10 months ago by
Michael Love
43k • written 2.1 years ago by
kiqbal
• 0
2
votes
3
replies
1.8k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
written 2.2 years ago by
L
▴ 50
6
votes
7
replies
3.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR
tximport
differential expression
updated 14 days ago by
Gordon Smyth
52k • written 4.7 years ago by
hollandademello
▴ 20
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 10 months ago by
Eva
• 0 • written 8.3 years ago by
ctl
• 0
16 results • Page
1 of 1
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
by
James W. MacDonald
67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue
by
k.panov
• 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package
by
Lukas
▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts
by
sindhuri
• 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package
by
James W. MacDonald
67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Awards
• All
Popular Question
to
Gordon Smyth
52k
Popular Question
to
linouhao
▴ 20
Popular Question
to
spg
• 0
Popular Question
to
otieno43
• 0
Popular Question
to
svlachavas
▴ 840
Locations
• All
Kazakhstan,
1 minute ago
The city by the bay,
1 hour ago
United KIngdom,
1 hour ago
EMBL Heidelberg,
2 hours ago
United States,
3 hours ago
Traffic: 611 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