Showing : salmon • reset
2
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6
replies
241
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Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
6 weeks ago • updated 4 weeks ago reganhayward • 0
2
votes
1
reply
163
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 9 weeks ago by 33k • written 10 weeks ago by • 0
1
vote
2
replies
232
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
5 months ago Nikolay Ivanov • 0
0
votes
7
replies
294
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 6 weeks ago by 33k • written 5 months ago by ▴ 10
0
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2
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142
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 5 months ago by 57k • written 5 months ago by • 0
0
votes
5
replies
223
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 11 months ago by 33k • written 11 months ago by • 0
2
votes
1
reply
193
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 12 months ago by 33k • written 12 months ago by ▴ 20
2
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2
replies
175
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
13 months ago • updated 12 months ago keremwai • 0
2
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3
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153
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 13 months ago by 33k • written 13 months ago by • 0
0
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3
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166
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 14 months ago by 33k • written 14 months ago by • 0
1
vote
3
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251
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 14 months ago by 33k • written 14 months ago by • 0
0
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4
replies
166
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon tximport tximportdata ensembl
updated 15 months ago by 33k • written 15 months ago by • 0
4
votes
0
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503
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
15 months ago Michael Love 33k
0
votes
6
replies
214
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 16 months ago by • 0 • written 16 months ago by • 0
0
votes
3
replies
347
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 17 months ago by 33k • written 17 months ago by • 0
0
votes
1
reply
219
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 18 months ago by 33k • written 18 months ago by • 0
0
votes
5
replies
185
views
Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport Gene IDs txdb RefSeq Salmon
updated 18 months ago by 33k • written 18 months ago by • 0
0
votes
5
replies
217
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
18 months ago omid.alamdari • 0
2
votes
11
replies
972
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
20 months ago • updated 19 months ago mico • 0
1
vote
3
replies
221
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 21 months ago by 3.2k • written 21 months ago by ▴ 10
0
votes
8
replies
431
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
22 months ago k1mukund • 0
1
vote
2
replies
224
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 22 months ago by 33k • written 22 months ago by ▴ 10
2
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3
replies
246
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 22 months ago by 33k • written 22 months ago by • 0
2
votes
7
replies
520
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 23 months ago by 57k • written 23 months ago by • 0
1
vote
1
reply
291
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
23 months ago konstantinos.bogias ▴ 10
5
votes
5
replies
1.6k
views
tximport transcript missing
deseq2 salmon tximport
2.0 years ago mr6518849 ▴ 10
0
votes
2
replies
303
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 2.1 years ago by 33k • written 2.1 years ago by ▴ 20
1
vote
3
replies
277
views
DESeq2 gives weird results
deseq2 salmon
updated 2.2 years ago by 33k • written 2.2 years ago by • 0
1
vote
1
reply
584
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.3 years ago by 33k • written 2.5 years ago by ▴ 10
1
vote
9
replies
733
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 2.3 years ago by ▴ 100 • written 2.3 years ago by • 0
1
vote
5
replies
738
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
updated 2.3 years ago by 33k • written 2.3 years ago by ▴ 10
2
votes
8
replies
441
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 2.3 years ago by 33k • written 2.3 years ago by • 0
3
votes
4
replies
377
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 2.3 years ago by 33k • written 2.3 years ago by ▴ 10
1
vote
1
reply
355
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 2.3 years ago by 33k • written 2.3 years ago by • 0
1
vote
6
replies
795
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 2.4 years ago by 33k • written 2.4 years ago by • 0
4
votes
10
replies
608
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 2.5 years ago by 33k • written 2.5 years ago by • 0
1
vote
3
replies
599
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 2.5 years ago by 33k • written 2.5 years ago by • 0
8
votes
4
replies
1.4k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 2.7 years ago by ★ 2.6k • written 2.7 years ago by ▴ 20
2
votes
3
replies
546
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 2.7 years ago by 33k • written 2.7 years ago by ▴ 20
1
vote
1
reply
302
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 2.7 years ago by 33k • written 2.7 years ago by ▴ 10
0
votes
0
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373
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
2.7 years ago lkianmehr • 0
1
vote
2
replies
395
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
2.8 years ago fcuy047 • 0
2
votes
7
replies
590
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 3.0 years ago by 33k • written 3.0 years ago by ▴ 20
2
votes
9
replies
599
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 10
0
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3
replies
1.1k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 3.2 years ago by ★ 1.9k • written 3.2 years ago by ▴ 30
1
vote
1
reply
494
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 3.2 years ago by 57k • written 3.2 years ago by • 0
0
votes
6
replies
438
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 3.2 years ago by 25k • written 3.2 years ago by • 0
1
vote
5
replies
2.0k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 3.2 years ago by 33k • written 4.2 years ago by • 0
1
vote
4
replies
871
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 3.3 years ago by 33k • written 3.3 years ago by ▴ 120
0
votes
1
reply
431
views
tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 3.4 years ago by 33k • written 3.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx for the advice about the reference levels, in which I did do as you suggested! In fact, I even tried more options just want to see why…
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels by Gordon Smyth 43k
> is there a way to incorporate also the information of the additional samples that lack any of the aforementioned levels? NA values are n…
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels by James W. MacDonald 57k
The `voomLmFit` function will automatically fit a linear mixed model accounting for within-subject correlations if you block on patient, so…
Comment: error in getBM (biomaRt): "error: no such table: metadata" by Mike Smith ★ 5.0k
Thanks for providing this solution. Anyone else encountering the issue can test if the cache is a problem by running `getBM()` with the ar…
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels by svlachavas ▴ 780
Dear James, thank you very much for your comment; please excuse me for my naïve additional question, but is there an example in the edgeR …
Votes
tximeta error in fetching genome info
Answer: error in getBM (biomaRt): "error: no such table: metadata"
C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Answer: cannot install edgeR on M1 Mac
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