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
2
votes
3
replies
335
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 6 weeks ago by
Vitor
• 0
4
votes
13
replies
530
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 days ago by
Michael Love
40k • written 5 weeks ago by
Christian
• 0
0
votes
4
replies
309
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 5 weeks ago by
Michael Love
40k • written 6 weeks ago by
hanc
• 0
1
vote
2
replies
283
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 9 weeks ago by
k.vitting.seerup
▴ 120 • written 9 weeks ago by
elva.gypsophila
▴ 10
2
votes
9
replies
629
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
3 months ago • updated 12 weeks ago
Ndimensional
▴ 20
0
votes
2
replies
309
views
tximport error in reading salmon output files?
tximport
tximportData
3 months ago
barrypraveen
• 0
0
votes
1
reply
312
views
Which file in tximport should I use for DESeq2 analysis?
tximport
DESeq2
updated 4 months ago by
James W. MacDonald
63k • written 4 months ago by
Yijing
• 0
2
votes
1
reply
315
views
scaledTPM for DESeq2 using tximport
DESeq2
tximport
updated 4 months ago by
Michael Love
40k • written 4 months ago by
prangannathofficial
• 0
3
votes
7
replies
590
views
failed to use tximport for creating count matrix from kallisto
tximport
kallisto
5 months ago • updated 4 months ago
Yijing
• 0
0
votes
2
replies
371
views
Error in H5Fopen
rhdf5
Rhdf5lib
kallisto
tximport
5 months ago
Yijing
• 0
1
vote
3
replies
419
views
tximport error
tximport
r
updated 5 months ago by
Michael Love
40k • written 5 months ago by
Joana
• 0
0
votes
2
replies
435
views
combining multiple salmon runs after tximport
tximport
RNASeq
salmon
updated 7 months ago by
ATpoint
★ 3.4k • written 7 months ago by
Ivana
• 0
1
vote
5
replies
661
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 7 months ago by
Michael Love
40k • written 7 months ago by
Michael Steinbaugh
▴ 90
3
votes
5
replies
778
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
7 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
404
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 8 months ago by
Dario Strbenac
★ 1.5k • written 8 months ago by
Hicham
▴ 10
0
votes
2
replies
491
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 8 months ago by
camilia.savitri
• 0
0
votes
1
reply
398
views
Missing transcript
DESeq2
tximport
salmon
updated 9 months ago by
ATpoint
★ 3.4k • written 9 months ago by
camilia.savitri
• 0
2
votes
1
reply
403
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 9 months ago by
ATpoint
★ 3.4k • written 9 months ago by
Dunois
• 0
2
votes
2
replies
653
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
written 9 months ago by
kiqbal
• 0
0
votes
2
replies
478
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
10 months ago
Konstantinos
• 0
2
votes
3
replies
762
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
10 months ago
mohammedtoufiq91
▴ 10
4
votes
3
replies
637
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene
tximport
Arabidopsis_thaliana
kallisto
updated 10 months ago by
James W. MacDonald
63k • written 10 months ago by
Mikhail Biryukov
▴ 10
0
votes
1
reply
547
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 10 months ago by
ATpoint
★ 3.4k • written 10 months ago by
Jenni
• 0
1
vote
2
replies
494
views
error loading kallisto output in tximport
file.exists
false
kallisto
tximport
10 months ago
cta
• 0
2
votes
2
replies
763
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
11 months ago
L
▴ 50
3
votes
3
replies
569
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport
tximportData
Quantseq
kallisto
11 months ago
duhwa.lee
• 0
1
vote
2
replies
882
views
transcripts missing from tx2gene
tximport
12 months ago
Erick
• 0
0
votes
1
reply
428
views
tximport: not all(file.exists(files)) are true
tximport
updated 12 months ago by
Michael Love
40k • written 12 months ago by
凯
• 0
2
votes
1
reply
868
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 12 months ago by
ATpoint
★ 3.4k • written 12 months ago by
Florent
▴ 10
3
votes
4
replies
677
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq
tximport
updated 12 months ago by
ATpoint
★ 3.4k • written 12 months ago by
snowmattin
• 0
0
votes
3
replies
612
views
tximport error
error
tximport
updated 12 months ago by
Michael Love
40k • written 13 months ago by
hana
• 0
5
votes
6
replies
967
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2
limma
tximport
updated 12 months ago by
Gordon Smyth
48k • written 13 months ago by
Kent
• 0
0
votes
4
replies
756
views
Alternative for wininet method in tximeta
DESeq2
tximport
tximportData
tximeta
15 months ago
uhlkatie
• 0
1
vote
3
replies
1.1k
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 15 months ago by
Michael Love
40k • written 15 months ago by
BG
• 0
2
votes
8
replies
1.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
15 months ago
Kelen
▴ 10
0
votes
1
reply
663
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 16 months ago by
ATpoint
★ 3.4k • written 16 months ago by
johnmcma
▴ 10
0
votes
1
reply
608
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport
R
updated 16 months ago by
Michael Love
40k • written 17 months ago by
cthangav
• 0
2
votes
3
replies
833
views
Problem with tximport IDs
tximport
tx2gene
rnas
DESeq2
RNASeqData
17 months ago
Maka
• 0
5
votes
4
replies
1.5k
views
confused with tximport counts abundance using salmon input
RNASeq
tximport
18 months ago
Al90
▴ 10
0
votes
2
replies
1.8k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux
R
tximport
19 months ago
nakane_clan
• 0
2
votes
5
replies
1.3k
views
from kallisto to deseq2 analysis
biomaRt
DESeq2
tximport
19 months ago
Marianna
▴ 10
2
votes
3
replies
732
views
Import RSEM output without sample data
DESeq2
tximportData
tximport
updated 19 months ago by
Michael Love
40k • written 20 months ago by
Luisa
• 0
0
votes
1
reply
546
views
tximport
salmon
tximport
updated 20 months ago by
Michael Love
40k • written 20 months ago by
Pragathi
• 0
0
votes
1
reply
658
views
Ensembl dataset version
tximport
rna
rnaseqGene
biomaRt
updated 21 months ago by
ATpoint
★ 3.4k • written 21 months ago by
st3472
• 0
0
votes
3
replies
1.0k
views
tximport question on what counts to use for LogFC calculations
tximport
updated 22 months ago by
Michael Love
40k • written 22 months ago by
mailmpunta
• 0
0
votes
4
replies
1.2k
views
Filtering output from tximport
tximport
Salmon
updated 22 months ago by
Michael Love
40k • written 22 months ago by
Sheean
• 0
0
votes
1
reply
966
views
tximport samples with separate tx2gene maps
tximport
updated 23 months ago by
Michael Love
40k • written 24 months ago by
nicolette.sipperly
• 0
1
vote
5
replies
2.2k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 11 weeks ago by
Michael Love
40k • written 23 months ago by
nicolette.sipperly
• 0
2
votes
1
reply
1.2k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2
tximport
Kallisto
TMM
edgeR
updated 24 months ago by
Michael Love
40k • written 24 months ago by
BioNovice247
• 0
0
votes
2
replies
1.1k
views
Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon
ignoreTxVersion
tximport
updated 2.1 years ago by
Michael Love
40k • written 2.1 years ago by
robeaumont
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results
by
James W. MacDonald
63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences
by
Hervé Pagès
16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results
by
camillab.
▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
Awards
• All
Popular Question
to
Yahan
• 0
Popular Question
to
Gordon Smyth
48k
Popular Question
to
Guido Hooiveld
★ 3.7k
Popular Question
to
camillab.
▴ 10
Popular Question
to
James W. MacDonald
63k
Locations
• All
WEHI, Melbourne, Australia,
4 minutes ago
Japan,
23 minutes ago
Melbourne, Australia,
30 minutes ago
United States,
1 hour ago
The city by the bay,
2 hours ago
Traffic: 336 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