Showing : tximport • reset
0
votes
4
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488
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
13 days ago • updated 3 days ago Nicholas • 0
0
votes
11
replies
803
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 8 weeks ago by • 0 • written 9 weeks ago by • 0
1
vote
2
replies
650
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
4
votes
5
replies
869
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
4 months ago LuciaNhu • 0
0
votes
2
replies
490
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
2
replies
495
views
tximport data import
tximport
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
2
replies
943
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
7 months ago grothmn • 0
0
votes
4
replies
704
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
9 months ago JG13 • 0
0
votes
2
replies
661
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
11 months ago Marianna ▴ 20
0
votes
2
replies
711
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 11 months ago by 43k • written 11 months ago by • 0
2
votes
1
reply
608
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 12 months ago by ★ 4.7k • written 12 months ago by • 0
0
votes
1
reply
836
views
tximport error with rsem files
rsem tximport
updated 15 months ago by ★ 4.7k • written 15 months ago by • 0
2
votes
3
replies
2.9k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
3
votes
2
replies
1.1k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
3
replies
963
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 17 months ago by 43k • written 17 months ago by • 0
10
votes
11
replies
3.0k
views
tximport error: vroom
tximport
updated 17 months ago by • 0 • written 17 months ago by ▴ 40
5
votes
13
replies
3.2k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
2
votes
4
replies
1.7k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 18 months ago by 43k • written 19 months ago by ▴ 10
2
votes
3
replies
1.3k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 19 months ago by • 0
1
vote
2
replies
2.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 19 months ago by ▴ 120 • written 20 months ago by ▴ 10
2
votes
9
replies
1.9k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
20 months ago Ndimensional ▴ 20
0
votes
2
replies
1.0k
views
tximport error in reading salmon output files?
tximport tximportData
updated 13 months ago by • 0 • written 21 months ago by • 0
0
votes
1
reply
975
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
2
votes
1
reply
1.1k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 22 months ago by 43k • written 22 months ago by • 0
3
votes
7
replies
1.7k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
22 months ago Yijing • 0
0
votes
2
replies
1.4k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
23 months ago • updated 22 months ago Yijing • 0
1
vote
3
replies
1.4k
views
tximport error
tximport r
updated 23 months ago by 43k • written 23 months ago by • 0
0
votes
2
replies
1.5k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by • 0
1
vote
5
replies
1.8k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 90
6
votes
10
replies
3.2k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 11 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.2 years ago by ★ 1.6k • written 2.2 years ago by ▴ 10
0
votes
2
replies
1.3k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.2 years ago by • 0
0
votes
1
reply
1.2k
views
Missing transcript
DESeq2 tximport salmon
updated 2.2 years ago by ★ 4.7k • written 2.2 years ago by • 0
2
votes
1
reply
1.1k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.2 years ago by ★ 4.7k • written 2.2 years ago by • 0
2
votes
5
replies
2.2k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 13 months ago by 43k • written 2.2 years ago by • 0
0
votes
2
replies
1.2k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.3 years ago Konstantinos • 0
2
votes
3
replies
1.8k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.3 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.6k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.3 years ago by ★ 4.7k • written 2.3 years ago by • 0
1
vote
2
replies
1.1k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.4 years ago cta • 0
2
votes
3
replies
1.9k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.4 years ago by ▴ 50
3
votes
3
replies
1.5k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.4 years ago duhwa.lee • 0
1
vote
2
replies
2.3k
views
transcripts missing from tx2gene
tximport
2.5 years ago Erick • 0
0
votes
1
reply
959
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
3
votes
1
reply
3.1k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.5 years ago by ★ 4.7k • written 2.5 years ago by ▴ 10
3
votes
4
replies
2.1k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.5 years ago by ★ 4.7k • written 2.5 years ago by • 0
0
votes
3
replies
1.3k
views
tximport error
error tximport
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
5
votes
6
replies
2.1k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.5 years ago by 52k • written 2.6 years ago by • 0
0
votes
4
replies
1.6k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.7 years ago uhlkatie • 0
2
votes
8
replies
2.1k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.7 years ago Kelen ▴ 10
50 results • Page 1 of 1
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa by Daniel • 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Votes
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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