Showing : salmon • reset
0
votes
2
replies
123
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 28 days ago by • 0
0
votes
1
reply
105
views
Missing transcript
DESeq2 tximport salmon
updated 4 weeks ago by ★ 2.1k • written 4 weeks ago by • 0
2
votes
1
reply
120
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Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 4 weeks ago by ★ 2.1k • written 4 weeks ago by • 0
2
votes
2
replies
159
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
written 6 weeks ago by • 0
0
votes
1
reply
142
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 11 weeks ago by ★ 2.1k • written 11 weeks ago by • 0
0
votes
2
replies
255
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
3 months ago manduchi ▴ 10
0
votes
1
reply
245
views
Adding custom transcript to Salmon index
salmon
updated 5 months ago by ★ 2.1k • written 5 months ago by • 0
1
vote
3
replies
604
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 11 months ago by 39k • written 12 months ago by • 0
0
votes
1
reply
347
views
tximport
salmon tximport
updated 12 months ago by 39k • written 12 months ago by • 0
1
vote
1
reply
821
views
TPM to raw counts
salmon DESeq2
updated 13 months ago by 13k • written 13 months ago by • 0
0
votes
4
replies
821
views
Filtering output from tximport
tximport Salmon
updated 14 months ago by 39k • written 14 months ago by • 0
2
votes
2
replies
866
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
17 months ago • updated 16 months ago Qin ▴ 10
0
votes
2
replies
723
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 17 months ago by 39k • written 17 months ago by • 0
0
votes
14
replies
1.3k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
18 months ago Abhishek • 0
2
votes
6
replies
2.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
20 months ago • updated 19 months ago reganhayward • 0
2
votes
1
reply
558
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 20 months ago by 39k • written 21 months ago by • 0
1
vote
2
replies
1.0k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
23 months ago Nikolay Ivanov • 0
0
votes
7
replies
996
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 20 months ago by 39k • written 23 months ago by ▴ 20
0
votes
2
replies
516
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 2.0 years ago by 62k • written 2.0 years ago by • 0
0
votes
5
replies
816
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 2.5 years ago by 39k • written 2.5 years ago by • 0
2
votes
1
reply
794
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 2.5 years ago by 39k • written 2.5 years ago by ▴ 20
2
votes
2
replies
592
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
2.6 years ago keremwai • 0
2
votes
3
replies
473
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 2.7 years ago by 39k • written 2.7 years ago by • 0
0
votes
3
replies
641
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 2.7 years ago by 39k • written 2.7 years ago by • 0
1
vote
3
replies
884
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 2.7 years ago by 39k • written 2.7 years ago by ▴ 10
0
votes
4
replies
542
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 2.8 years ago by 39k • written 2.8 years ago by • 0
4
votes
0
replies
1.3k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
2.8 years ago Michael Love 39k
0
votes
6
replies
559
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
0
votes
3
replies
1.5k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 3.0 years ago by 39k • written 3.0 years ago by • 0
0
votes
1
reply
675
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 3.0 years ago by 39k • written 3.0 years ago by • 0
0
votes
5
replies
945
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 3.0 years ago by 39k • written 3.0 years ago by • 0
0
votes
5
replies
634
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
3.1 years ago omid.alamdari • 0
2
votes
11
replies
1.9k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
3.2 years ago mico • 0
1
vote
3
replies
447
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 3.3 years ago by 3.7k • written 3.3 years ago by ▴ 10
0
votes
8
replies
1.7k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
3.4 years ago k1m ▴ 10
1
vote
2
replies
512
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 3.4 years ago by 39k • written 3.4 years ago by ▴ 10
2
votes
3
replies
703
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 3.4 years ago by 39k • written 3.4 years ago by • 0
2
votes
7
replies
1.2k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 3.4 years ago by 62k • written 3.4 years ago by • 0
1
vote
1
reply
591
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
3.5 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
3.4k
views
tximport transcript missing
deseq2 salmon tximport
3.5 years ago mr6518849 ▴ 10
0
votes
2
replies
525
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 3.6 years ago by 39k • written 3.6 years ago by ▴ 20
1
vote
3
replies
637
views
DESeq2 gives weird results
deseq2 salmon
updated 3.7 years ago by 39k • written 3.7 years ago by • 0
1
vote
1
reply
905
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 3.8 years ago by 39k • written 4.1 years ago by ▴ 10
1
vote
9
replies
1.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 3.8 years ago by ▴ 120 • written 3.8 years ago by • 0
1
vote
5
replies
1.6k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
updated 3.8 years ago by 39k • written 3.8 years ago by ▴ 10
2
votes
8
replies
869
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 3.9 years ago by 39k • written 3.9 years ago by • 0
3
votes
4
replies
905
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 3.9 years ago by 39k • written 3.9 years ago by ▴ 10
1
vote
1
reply
639
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 3.9 years ago by 39k • written 3.9 years ago by • 0
1
vote
6
replies
1.4k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 3.9 years ago by 39k • written 3.9 years ago by • 0
4
votes
10
replies
1.5k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 4.0 years ago by 39k • written 4.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Jonathan Göke ▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R by Gordon Smyth 47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user) by lalanis1 • 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma by Gordon Smyth 47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Comment: Question about GWASTools gdsSubset by Stephanie M. Gogarten ▴ 840
You could see if an attribute has been set on the genotype node indicating the order: ``` > library(gdsfmt) > gdsfile <- system.file("extda…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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