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 :
txImportData
•
reset
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
631
views
tximport error in reading salmon output files?
tximport
tximportData
updated 11 weeks ago by
Matteo
• 0 • written 10 months ago by
barrypraveen
• 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
3
votes
3
replies
898
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
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
21 months ago
uhlkatie
• 0
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
0
votes
3
replies
906
views
tximport fails when RSEM output options produce files with additional columns?
DESeq2
tximportData
tximpor
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
Alexander
• 0
0
votes
1
reply
832
views
Multi-factor Analysis in DeSEQ2
tximport
R
tximportData
RNASeq
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
pthom010
• 0
0
votes
7
replies
1.7k
views
Problem with Tximport
tximportData
tximport
3.2 years ago
agoesmartini
• 0
0
votes
1
reply
909
views
How to use tx import on output of abundance file
tximportData
tximport
updated 3.4 years ago by
Kevin Blighe
★ 3.9k • written 3.4 years ago by
Julie
• 0
0
votes
4
replies
1.1k
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon
tximport
tximportdata
ensembl
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
slouis
• 0
1
vote
2
replies
1.0k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
5.5 years ago
fcuy047
• 0
1
vote
2
replies
1.2k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
Stanley Yang
• 0
1
vote
8
replies
33k
views
How to create tx2gene.gencode.v27.csv
tximportdata
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
mmokrejs
• 0
2
votes
6
replies
1.6k
views
[DESeq2] Different results from tutorial
deseq2
tximportdata
tximport
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
changhan1110
• 0
0
votes
1
reply
2.3k
views
could not find function "tximport"
tximportdata
updated 6.1 years ago by
Gordon Smyth
50k • written 6.1 years ago by
s.corley
▴ 30
0
votes
9
replies
3.5k
views
Upgrade bioconductor 3.2 to 3.3
bioclIte
tximportData
updated 6.2 years ago by
hauken_heyken
▴ 80 • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
0
votes
3
replies
13k
views
Problem installing tximportData
tximportdata
7.1 years ago
elg
• 0
3
votes
5
replies
2.7k
views
txImport: a gene seems missing from the sample data
txImportData
txImport
updated 3.2 years ago by
James W. MacDonald
65k • written 7.1 years ago by
alexlok
• 0
0
votes
1
reply
1.7k
views
How to remove genes with 0 counts in tximport?
tximport
deseq
tximportdata
deseq2
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
Peter Alto
▴ 10
0
votes
7
replies
1.7k
views
PCA results different from th same sample but different counting method
deseq2
pca
tximportdata
htseqcounts
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
21 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Awards
• All
Popular Question
to
shepherl
3.8k
Popular Question
to
BioinfGuru
▴ 20
Popular Question
to
Gordon Smyth
50k
Scholar
to
Peter Hickey
▴ 740
Popular Question
to
sropri
• 0
Locations
• All
United States,
2 minutes ago
Netherlands,
9 minutes ago
France/Marseille/Inserm,
16 minutes ago
France,
18 minutes ago
UPF, Barcelona, Spain,
34 minutes ago
Traffic: 718 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