Showing : Salmon • reset
0
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4
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1.4k
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How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
6.7 years ago bruno.saubamea • 0
0
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2
replies
948
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
2
votes
9
replies
1.3k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
0
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6
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2.9k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
6.9 years ago sunil.mangalam • 0
2
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2
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1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.8 years ago keremwai • 0
12
votes
4
replies
3.8k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by ▴ 30
0
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2
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800
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
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1
reply
1.2k
views
salmon quantification - identical transcripts in fasta file
salmon
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 30
1
vote
5
replies
2.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 70
1
vote
5
replies
3.2k
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tximport using for data generated from other tools
tximport salmon eXpress
updated 6.0 years ago by 41k • written 6.9 years ago by • 0
2
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3
replies
2.5k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
4
votes
3
replies
3.4k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 2.3 years ago by • 0 • written 6.8 years ago by • 0
1
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5
replies
2.0k
views
tximport error with salmon version
deseq2 salmon tximport
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
1
vote
4
replies
1.4k
views
Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
salmon tximport limma-voom
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 30
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 30
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
5
votes
9
replies
3.5k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.2 years ago emmak ▴ 20
0
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2
replies
2.4k
views
use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
0
votes
1
reply
865
views
tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 6.1 years ago by 41k • written 6.1 years ago by • 0
1
vote
4
replies
2.1k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 120
0
votes
6
replies
1.0k
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 6.0 years ago by 25k • written 6.0 years ago by • 0
1
vote
1
reply
1.2k
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
0
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3
replies
4.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 6.0 years ago by ★ 2.0k • written 6.0 years ago by ▴ 30
2
votes
7
replies
1.6k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 5.8 years ago by 41k • written 5.8 years ago by ▴ 20
1
vote
2
replies
1.0k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
5.5 years ago fcuy047 • 0
1
vote
1
reply
888
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
0
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3
replies
427
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
5
votes
9
replies
5.3k
views
Trouble with Tximport
tximport salmon
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 30
1
vote
4
replies
1.4k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
7.8 years ago Assa Yeroslaviz ★ 1.5k
1
vote
5
replies
1.8k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 7.6 years ago by 41k • written 7.6 years ago by • 0
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 30
2
votes
7
replies
2.6k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
1
vote
4
replies
2.1k
views
tximport error reading salmon quantification files...
tximport salmon
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 20
0
votes
3
replies
305
views
Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 3 months ago by 41k • written 3 months ago by • 0
0
votes
4
replies
1.5k
views
Filtering output from tximport
tximport Salmon
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
1
vote
2
replies
1.5k
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
6
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10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 14 days ago by • 0 • written 15 months ago by ▴ 10
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 41k • written 12 months ago by ▴ 10
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.0 years ago by 41k • written 4.0 years ago by ▴ 10
2
votes
3
replies
1.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 30
1
vote
3
replies
1.6k
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
1
vote
1
reply
1.4k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 5.0 years ago by 41k • written 5.3 years ago by ▴ 60
4
votes
10
replies
2.8k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
2
votes
6
replies
2.0k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 5.1 years ago by 41k • written 5.2 years ago by • 0
1
vote
1
reply
1.0k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
3
votes
4
replies
1.7k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 10
2
votes
8
replies
1.6k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
1
vote
9
replies
2.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 5.1 years ago by ▴ 120 • written 5.1 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq2 gives weird results
deseq2 salmon
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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