Showing : Salmon • reset
0
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45
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Adding custom transcript to Salmon index
salmon
updated 2 days ago by ★ 1.4k • written 2 days ago by • 0
1
vote
3
replies
373
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 6 months ago by 37k • written 6 months ago by • 0
0
votes
1
reply
205
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tximport
salmon tximport
updated 6 months ago by 37k • written 6 months ago by • 0
1
vote
1
reply
222
views
TPM to raw counts
salmon DESeq2
updated 7 months ago by 13k • written 7 months ago by • 0
0
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4
replies
577
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Filtering output from tximport
tximport Salmon
updated 9 months ago by 37k • written 9 months ago by • 0
2
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2
replies
553
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
11 months ago • updated 10 months ago Qin ▴ 10
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2
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475
views
Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon ignoreTxVersion tximport
updated 11 months ago by 37k • written 11 months ago by • 0
0
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14
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1.0k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
12 months ago Abhishek • 0
2
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6
replies
1.4k
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Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
14 months ago reganhayward • 0
2
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1
reply
399
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 15 months ago by 37k • written 15 months ago by • 0
1
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2
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724
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
17 months ago Nikolay Ivanov • 0
0
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7
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782
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Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 14 months ago by 37k • written 18 months ago by ▴ 10
0
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2
replies
391
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 18 months ago by 60k • written 18 months ago by • 0
0
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5
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678
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 2.0 years ago by 37k • written 2.0 years ago by • 0
2
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1
reply
543
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 2.0 years ago by 37k • written 2.0 years ago by ▴ 20
2
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2
replies
472
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
2.1 years ago keremwai • 0
2
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3
replies
362
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 2.2 years ago by 37k • written 2.2 years ago by • 0
0
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3
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450
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 2.2 years ago by 37k • written 2.2 years ago by • 0
1
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3
replies
663
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 2.3 years ago by 37k • written 2.3 years ago by ▴ 10
0
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4
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395
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 2.3 years ago by 37k • written 2.3 years ago by • 0
4
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0
replies
1.1k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
2.3 years ago Michael Love 37k
0
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6
replies
453
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
0
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3
replies
1.1k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 2.5 years ago by 37k • written 2.5 years ago by • 0
0
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1
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555
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 2.5 years ago by 37k • written 2.5 years ago by • 0
0
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5
replies
646
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 2.6 years ago by 37k • written 2.6 years ago by • 0
0
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5
replies
487
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
2.6 years ago omid.alamdari • 0
2
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11
replies
1.7k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
2.8 years ago • updated 2.7 years ago mico • 0
1
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3
replies
371
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RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 2.8 years ago by 3.6k • written 2.8 years ago by ▴ 10
0
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8
replies
1.2k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
2.9 years ago k1mukund • 0
1
vote
2
replies
422
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 2.9 years ago by 37k • written 2.9 years ago by ▴ 10
2
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3
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543
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 2.9 years ago by 37k • written 2.9 years ago by • 0
2
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7
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1.1k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 3.0 years ago by 60k • written 3.0 years ago by • 0
1
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1
reply
503
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
3.0 years ago konstantinos.bogias ▴ 10
5
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5
replies
2.8k
views
tximport transcript missing
deseq2 salmon tximport
3.1 years ago mr6518849 ▴ 10
0
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2
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438
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Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 3.2 years ago by 37k • written 3.2 years ago by ▴ 20
1
vote
3
replies
498
views
DESeq2 gives weird results
deseq2 salmon
updated 3.2 years ago by 37k • written 3.2 years ago by • 0
1
vote
1
reply
812
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 3.3 years ago by 37k • written 3.6 years ago by ▴ 10
1
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9
replies
1.3k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 3.4 years ago by ▴ 120 • written 3.4 years ago by • 0
1
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5
replies
1.3k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
updated 3.4 years ago by 37k • written 3.4 years ago by ▴ 10
2
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8
replies
714
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 3.4 years ago by 37k • written 3.4 years ago by • 0
3
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4
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730
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 3.4 years ago by 37k • written 3.4 years ago by ▴ 10
1
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1
reply
550
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 3.4 years ago by 37k • written 3.4 years ago by • 0
1
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6
replies
1.3k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 3.4 years ago by 37k • written 3.4 years ago by • 0
4
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10
replies
1.1k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 3.6 years ago by 37k • written 3.6 years ago by • 0
1
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3
replies
965
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 3.6 years ago by 37k • written 3.6 years ago by • 0
8
votes
4
replies
2.1k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 3.7 years ago by ★ 2.7k • written 3.7 years ago by ▴ 20
2
votes
3
replies
961
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 3.7 years ago by 37k • written 3.7 years ago by ▴ 20
1
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1
reply
479
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 3.7 years ago by 37k • written 3.7 years ago by ▴ 10
0
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0
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555
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
3.8 years ago lkianmehr • 0
1
vote
2
replies
598
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What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
3.8 years ago fcuy047 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: mapToAlignments_issue by Hervé Pagès 15k
> I would expect in case of reverse alignment lifted ranges to correspond to position 91-100 of the query sequence. Nope. Local coordinate…
Answer: Problem related to `biomaRt::getBM()` during `R CMD check` execution by James W. MacDonald 60k
Does the section in the biomaRt vignette that talks about caching (and using a temp dir) help?
Comment: OPLS-DA: confidence interval for accuracy metric by Eddie • 0
Worked well under pROC. Thank you
Comment: errors in annotation by James W. MacDonald 60k
If you go to NCBI and the data appear to be correct, then they have evidently already fixed the errors you have found. The data we download…
Comment: How should I set my eps value in cluster profiler? by Guido Hooiveld ★ 3.3k
Under the hood `clusterProfiler` makes use of a (fast) GSEA algorithm implemented in the package `fgsea` (function `fgseaMultilevel`). The …
Votes
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
How to select summit size for histone ChiP-Seq in Diffbind
Comment: GSEA with Wikipathways not entirely reproducible
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