Showing : TXIMPORT • reset
4
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5
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564
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
17 days ago LuciaNhu • 0
0
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2
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343
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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2
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391
views
tximport data import
tximport
updated 11 weeks ago by 42k • written 11 weeks ago by • 0
1
vote
2
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744
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
3 months ago grothmn • 0
1
vote
2
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2.2k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 5 months ago by ▴ 40 • written 5.1 years ago by • 0
0
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4
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571
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
5 months ago JG13 • 0
0
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2
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510
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
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2
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540
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 months ago by 42k • written 8 months ago by • 0
2
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1
reply
475
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 8 months ago by ★ 4.5k • written 8 months ago by • 0
2
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3
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2.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
0
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1
reply
669
views
tximport error with rsem files
rsem tximport
updated 11 months ago by ★ 4.5k • written 11 months ago by • 0
3
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2
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944
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 12 months ago by 67k • written 12 months ago by • 0
0
votes
3
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765
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 13 months ago by 42k • written 13 months ago by • 0
10
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11
replies
2.7k
views
tximport error: vroom
tximport
updated 13 months ago by • 0 • written 13 months ago by ▴ 40
2
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3
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1.2k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 15 months ago by • 0
4
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13
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2.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 14 months ago by 42k • written 15 months ago by • 0
0
votes
4
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1.4k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 15 months ago by 42k • written 15 months ago by • 0
1
vote
2
replies
2.2k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 16 months ago by ▴ 120 • written 16 months ago by ▴ 10
2
votes
9
replies
1.7k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
16 months ago Ndimensional ▴ 20
0
votes
2
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904
views
tximport error in reading salmon output files?
tximport tximportData
updated 9 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
884
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 18 months ago by 67k • written 18 months ago by • 0
2
votes
1
reply
976
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 18 months ago by 42k • written 18 months ago by • 0
3
votes
7
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1.5k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
19 months ago • updated 18 months ago Yijing • 0
0
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2
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1.2k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
19 months ago Yijing • 0
1
vote
3
replies
1.2k
views
tximport error
tximport r
updated 19 months ago by 42k • written 19 months ago by • 0
0
votes
2
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1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 21 months ago by ★ 4.5k • written 21 months ago by • 0
1
vote
5
replies
1.6k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 21 months ago by 42k • written 21 months ago by ▴ 90
6
votes
10
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2.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 months ago by • 0 • written 21 months ago by ▴ 10
0
votes
1
reply
945
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 10
0
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2
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1.1k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 22 months ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
2
votes
1
reply
971
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
2
votes
5
replies
1.9k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 months ago by 42k • written 23 months ago by • 0
0
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2
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1.0k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
24 months ago Konstantinos • 0
2
votes
3
replies
1.6k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
24 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.0 years ago by 67k • written 2.0 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.0 years ago by ★ 4.5k • written 2.0 years ago by • 0
1
vote
2
replies
1.0k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.0 years ago cta • 0
2
votes
3
replies
1.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.1 years ago by ▴ 50
3
votes
3
replies
1.3k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.1 years ago duhwa.lee • 0
1
vote
2
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2.0k
views
transcripts missing from tx2gene
tximport
2.2 years ago Erick • 0
0
votes
1
reply
866
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
2
votes
1
reply
2.5k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by ▴ 10
3
votes
4
replies
1.8k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by • 0
0
votes
3
replies
1.2k
views
tximport error
error tximport
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
5
votes
6
replies
1.9k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
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4
replies
1.4k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.4 years ago uhlkatie • 0
1
vote
3
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2.2k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.4 years ago Kelen ▴ 10
0
votes
1
reply
1.3k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.5 years ago by ★ 4.5k • written 2.5 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Answer: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
Yes. Samples in columns and genes in rows.
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k
It's not informative except for me to say I was right that it's `getSeq` that is providing the error. It appears that `AddMotifs` is passin…
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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