Showing : txImport • reset
0
votes
2
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144
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 days ago Marianna ▴ 20
0
votes
2
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191
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 29 days ago by 41k • written 29 days ago by • 0
2
votes
1
reply
233
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
votes
1
reply
317
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
2
votes
3
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1.1k
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
3
votes
2
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545
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
0
votes
3
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410
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 months ago by 41k • written 6 months ago by • 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 6 months ago by ▴ 40
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 7 months ago by • 0
0
votes
4
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848
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 7 months ago by 41k • written 8 months ago by • 0
2
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3
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794
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 9 months ago by ▴ 10
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
0
votes
2
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641
views
tximport error in reading salmon output files?
tximport tximportData
updated 11 weeks ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
591
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
2
votes
1
reply
638
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
11 months ago Yijing • 0
0
votes
2
replies
809
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago • updated 11 months ago Yijing • 0
1
vote
3
replies
845
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
2
replies
903
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 14 months ago by 41k • written 14 months ago by ▴ 90
6
votes
10
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1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 5 days ago by • 0 • written 14 months ago by ▴ 10
0
votes
1
reply
711
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 15 months ago by ★ 1.5k • written 15 months ago by ▴ 10
0
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2
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780
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 15 months ago by • 0
0
votes
1
reply
725
views
Missing transcript
DESeq2 tximport salmon
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
2
votes
1
reply
661
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 8 weeks ago by 41k • written 16 months ago by • 0
0
votes
2
replies
773
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
16 months ago Konstantinos • 0
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 months ago • updated 16 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.0k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 17 months ago by 65k • written 17 months ago by ▴ 10
0
votes
1
reply
882
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
1
vote
2
replies
778
views
error loading kallisto output in tximport
file.exists false kallisto tximport
17 months ago cta • 0
2
votes
2
replies
1.2k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
18 months ago L ▴ 50
3
votes
3
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908
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
1
vote
2
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1.5k
views
transcripts missing from tx2gene
tximport
19 months ago Erick • 0
0
votes
1
reply
621
views
tximport: not all(file.exists(files)) are true
tximport
updated 19 months ago by 41k • written 19 months ago by • 0
2
votes
1
reply
1.5k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 19 months ago by ★ 4.0k • written 19 months ago by ▴ 10
3
votes
4
replies
1.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
0
votes
3
replies
957
views
tximport error
error tximport
updated 19 months ago by 41k • written 19 months ago by • 0
5
votes
6
replies
1.4k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 19 months ago by 50k • written 20 months ago by • 0
0
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4
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1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
22 months ago uhlkatie • 0
2
votes
8
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1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
1
vote
3
replies
1.6k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 22 months ago by 41k • written 22 months ago by • 0
0
votes
1
reply
992
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 23 months ago by ★ 4.0k • written 23 months ago by ▴ 10
0
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1
reply
839
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 23 months ago by 41k • written 23 months ago by • 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
24 months ago Maka • 0
5
votes
4
replies
2.2k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.0 years ago Al90 ▴ 10
0
votes
2
replies
2.4k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
2.2 years ago nakane_clan • 0
2
votes
5
replies
1.7k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.2 years ago Marianna ▴ 20
2
votes
3
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947
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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