Showing : Salmon • reset
0
votes
3
replies
326
views
Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
3
replies
454
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 7 months ago by 42k • written 7 months ago by • 0
1
vote
2
replies
1.6k
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
0
votes
3
replies
712
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 11 months ago by 42k • written 11 months ago by • 0
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 13 months ago by 42k • written 13 months ago by ▴ 10
0
votes
2
replies
949
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 weeks ago by • 0 • written 15 months ago by ▴ 10
0
votes
2
replies
832
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
771
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
1
reply
712
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 12 weeks ago by 42k • written 17 months ago by • 0
0
votes
1
reply
916
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
0
votes
2
replies
1.0k
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
19 months ago manduchi ▴ 10
4
votes
1
reply
1.1k
views
Adding custom transcript to Salmon index
salmon
updated 21 months ago by ★ 4.1k • written 21 months ago by ▴ 20
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
1
reply
729
views
tximport
salmon tximport
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
1
vote
2
replies
2.9k
views
TPM to raw counts
salmon DESeq2
updated 5 months ago by • 0 • written 2.4 years ago by • 0
0
votes
4
replies
1.6k
views
Filtering output from tximport
tximport Salmon
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
2
votes
2
replies
2.1k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
2.7 years ago Qin ▴ 10
0
votes
2
replies
1.4k
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 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
14
replies
2.3k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
2.8 years ago Abhishek • 0
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.9 years ago reganhayward • 0
2
votes
1
reply
1.0k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
1
vote
2
replies
2.2k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
3.2 years ago Nikolay Ivanov • 0
0
votes
7
replies
2.0k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 3.0 years ago by 42k • written 3.3 years ago by ▴ 30
0
votes
2
replies
956
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.3 years ago by 66k • written 3.3 years ago by • 0
0
votes
5
replies
1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
2
votes
1
reply
1.5k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 20
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.9 years ago keremwai • 0
2
votes
3
replies
937
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
0
votes
3
replies
1.3k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
1
vote
3
replies
1.6k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 10
0
votes
4
replies
1.1k
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 4.1 years ago by 42k • written 4.1 years ago by • 0
4
votes
0
replies
2.1k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.1 years ago Michael Love 42k
0
votes
6
replies
1.1k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
0
votes
3
replies
2.6k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
0
votes
1
reply
1.1k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
0
votes
5
replies
2.0k
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 4.3 years ago by 42k • written 4.3 years ago by • 0
0
votes
5
replies
1.3k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
4.4 years ago omid.alamdari • 0
2
votes
11
replies
3.1k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
4.5 years ago mico • 0
1
vote
3
replies
880
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by ▴ 10
1
vote
8
replies
2.9k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.7 years ago k1m ▴ 20
1
vote
2
replies
943
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 4.7 years ago by 42k • written 4.7 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 4.7 years ago by 42k • written 4.7 years ago by • 0
2
votes
7
replies
2.0k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 4.7 years ago by 66k • written 4.7 years ago by • 0
1
vote
1
reply
980
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
4.8 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
4.9k
views
tximport transcript missing
deseq2 salmon tximport
4.8 years ago mr6518849 ▴ 10
0
votes
2
replies
963
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 4.9 years ago by 42k • written 4.9 years ago by ▴ 40
1
vote
3
replies
1.2k
views
DESeq2 gives weird results
deseq2 salmon
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
1
vote
1
reply
1.4k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 5.1 years ago by 42k • written 5.4 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue by Tahirah • 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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