Showing : tximport • reset
0
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10
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290
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
1 day ago • updated 2 hours ago brown.annaleigh • 0
1
vote
2
replies
474
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 weeks ago georgii.vdovin • 0
4
votes
5
replies
675
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 weeks ago LuciaNhu • 0
0
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2
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413
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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 3 months ago by 43k • written 3 months ago by • 0
0
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2
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441
views
tximport data import
tximport
updated 4 months ago by 43k • written 4 months ago by • 0
1
vote
2
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824
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
5 months ago grothmn • 0
1
vote
2
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2.3k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 7 months ago by ▴ 40 • written 5.2 years ago by • 0
0
votes
4
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630
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
7 months ago JG13 • 0
0
votes
2
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580
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
9 months ago Marianna ▴ 20
0
votes
2
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619
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 9 months ago by 43k • written 9 months ago by • 0
2
votes
1
reply
530
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
2
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3
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2.5k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
0
votes
1
reply
739
views
tximport error with rsem files
rsem tximport
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
3
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2
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1.0k
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 13 months ago by 67k • written 13 months ago by • 0
0
votes
3
replies
839
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 15 months ago by 43k • written 15 months ago by • 0
10
votes
11
replies
2.8k
views
tximport error: vroom
tximport
updated 14 months ago by • 0 • written 15 months ago by ▴ 40
2
votes
3
replies
1.2k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 17 months ago by • 0
4
votes
13
replies
2.8k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 15 months ago by 43k • written 16 months ago by • 0
0
votes
4
replies
1.5k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 16 months ago by 43k • written 17 months ago by • 0
1
vote
2
replies
2.3k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 17 months ago by ▴ 120 • written 18 months ago by ▴ 10
2
votes
9
replies
1.8k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
18 months ago Ndimensional ▴ 20
0
votes
2
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950
views
tximport error in reading salmon output files?
tximport tximportData
updated 11 months ago by • 0 • written 19 months ago by • 0
0
votes
1
reply
922
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 20 months ago by 67k • written 20 months ago by • 0
2
votes
1
reply
1.1k
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 20 months ago by 43k • written 20 months ago by • 0
3
votes
7
replies
1.6k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
20 months ago Yijing • 0
0
votes
2
replies
1.3k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
21 months ago • updated 20 months ago Yijing • 0
1
vote
3
replies
1.3k
views
tximport error
tximport r
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
2
replies
1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
1
vote
5
replies
1.7k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 23 months ago by 43k • written 23 months ago by ▴ 90
6
votes
10
replies
2.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 9 months ago by • 0 • written 23 months ago by ▴ 10
0
votes
1
reply
985
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.0 years ago by ★ 1.5k • written 2.0 years ago by ▴ 10
0
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2
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1.2k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
votes
1
reply
1.0k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
votes
5
replies
2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 11 months ago by 43k • written 2.1 years ago by • 0
0
votes
2
replies
1.1k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
2.1 years ago Konstantinos • 0
2
votes
3
replies
1.7k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2.1 years ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.5k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.2 years ago by 67k • written 2.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by • 0
1
vote
2
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1.1k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.2 years ago cta • 0
2
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3
replies
1.8k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.2 years ago by ▴ 50
3
votes
3
replies
1.4k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.3 years ago • updated 2.2 years ago duhwa.lee • 0
1
vote
2
replies
2.1k
views
transcripts missing from tx2gene
tximport
2.3 years ago Erick • 0
0
votes
1
reply
907
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
3
votes
1
reply
2.7k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by ▴ 10
3
votes
4
replies
1.9k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
0
votes
3
replies
1.3k
views
tximport error
error tximport
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
5
votes
6
replies
2.0k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
0
votes
4
replies
1.5k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.6 years ago uhlkatie • 0
1
vote
3
replies
2.3k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
50 results • Page 1 of 1
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Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by Jonathan ▴ 10
Thank you; I was indeed using `DGEList` on the count matrix, but with the multiple edits of the post I forgot to include this step. BTW, …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
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