Showing : tximport • reset
0
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2
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197
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
2
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216
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
2
votes
1
reply
270
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 9 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
2
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3
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1.3k
views
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 ★ 1.4k • written 5 months ago by • 0
0
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1
reply
368
views
tximport error with rsem files
rsem tximport
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
3
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2
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584
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
0
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3
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449
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 7 months ago by 42k • written 7 months ago by • 0
10
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11
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2.0k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
2
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3
replies
840
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
4
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13
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1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 42k • written 8 months ago by • 0
0
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4
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920
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 42k • written 9 months ago by • 0
1
vote
2
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1.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 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
10 months ago Ndimensional ▴ 20
0
votes
2
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684
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
638
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 12 months ago by 65k • written 12 months ago by • 0
2
votes
1
reply
675
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 12 months ago by 42k • written 12 months ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
0
votes
2
replies
851
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago Yijing • 0
1
vote
3
replies
889
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
0
votes
2
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944
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 15 months ago by 42k • written 15 months ago by ▴ 90
6
votes
10
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1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 29 days ago by • 0 • written 15 months ago by ▴ 10
0
votes
1
reply
748
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 16 months ago by ★ 1.5k • written 16 months ago by ▴ 10
0
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2
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823
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
766
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
1
reply
706
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 12 weeks ago by 42k • written 16 months ago by • 0
0
votes
2
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801
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
17 months ago Konstantinos • 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.1k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 18 months ago by 65k • written 18 months ago by ▴ 10
0
votes
1
reply
912
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
1
vote
2
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808
views
error loading kallisto output in tximport
file.exists false kallisto tximport
18 months ago cta • 0
2
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2
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1.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
19 months ago L ▴ 50
3
votes
3
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960
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
19 months ago • updated 18 months ago duhwa.lee • 0
1
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2
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1.5k
views
transcripts missing from tx2gene
tximport
20 months ago Erick • 0
0
votes
1
reply
647
views
tximport: not all(file.exists(files)) are true
tximport
updated 20 months ago by 42k • written 20 months ago by • 0
2
votes
1
reply
1.6k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 20 months ago by ★ 4.1k • written 20 months ago by ▴ 10
3
votes
4
replies
1.3k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
0
votes
3
replies
992
views
tximport error
error tximport
updated 20 months ago by 42k • written 20 months ago by • 0
5
votes
6
replies
1.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 20 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
1
vote
3
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1.7k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 23 months ago by 42k • written 23 months ago by • 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
23 months ago • updated 22 months ago Kelen ▴ 10
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 24 months ago by ★ 4.1k • written 2.0 years ago by ▴ 10
0
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1
reply
862
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 2.0 years ago by 42k • written 2.0 years ago by • 0
2
votes
3
replies
1.2k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
2.0 years ago Maka • 0
6
votes
4
replies
2.4k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.1 years ago Al90 ▴ 10
0
votes
2
replies
2.5k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
2.2 years ago nakane_clan • 0
2
votes
5
replies
1.8k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.3 years ago • updated 2.2 years ago Marianna ▴ 20
2
votes
3
replies
972
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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