Showing : Tximport • reset
0
votes
2
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144
views
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
2
votes
3
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1.1k
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 ★ 1.3k • written 4 months ago by • 0
0
votes
1
reply
319
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
3
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2
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546
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
replies
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
2
votes
3
replies
794
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
4
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13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
0
votes
4
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850
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 7 months ago by 41k • written 8 months ago by • 0
1
vote
2
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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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642
views
tximport error in reading salmon output files?
tximport tximportData
updated 12 weeks ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
592
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
639
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
811
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago • updated 11 months ago Yijing • 0
1
vote
3
replies
847
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
2
replies
905
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
replies
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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781
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
774
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
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779
views
error loading kallisto output in tximport
file.exists false kallisto tximport
17 months ago cta • 0
2
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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
replies
910
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
622
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
958
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
1
vote
3
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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
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
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
840
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 23 months ago by 41k • written 24 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
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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
1.8k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.2 years ago Marianna ▴ 20
2
votes
3
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948
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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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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