Showing : Salmon • reset
0
votes
3
replies
301
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
3
replies
424
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
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
0
votes
3
replies
677
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 41k • written 10 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 12 months ago by 41k • written 12 months ago by ▴ 10
0
votes
2
replies
920
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 12 days ago by • 0 • written 14 months ago by ▴ 10
0
votes
2
replies
794
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 15 months ago by • 0
0
votes
1
reply
738
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
2
votes
1
reply
675
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 9 weeks ago by 41k • written 16 months ago by • 0
0
votes
1
reply
891
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
votes
2
replies
971
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
18 months ago manduchi ▴ 10
4
votes
1
reply
1.1k
views
Adding custom transcript to Salmon index
salmon
updated 20 months ago by ★ 4.1k • written 20 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 2.2 years ago by 41k • written 2.2 years ago by • 0
0
votes
1
reply
713
views
tximport
salmon tximport
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
1
vote
2
replies
2.8k
views
TPM to raw counts
salmon DESeq2
updated 5 months ago by • 0 • written 2.3 years ago by • 0
0
votes
4
replies
1.5k
views
Filtering output from tximport
tximport Salmon
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
2
votes
2
replies
2.0k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
2.6 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 41k • 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 • updated 2.7 years ago Abhishek • 0
2
votes
6
replies
4.5k
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 41k • written 3.0 years ago by • 0
1
vote
2
replies
2.1k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
3.2 years ago Nikolay Ivanov • 0
0
votes
7
replies
1.9k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 2.9 years ago by 41k • written 3.2 years ago by ▴ 30
0
votes
2
replies
945
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.2 years ago by 65k • written 3.2 years ago by • 0
0
votes
5
replies
1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.7 years ago by 41k • written 3.7 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 41k • 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
3.8 years ago keremwai • 0
2
votes
3
replies
926
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 3.9 years ago by 41k • written 3.9 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 3.9 years ago by 41k • written 3.9 years ago by • 0
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
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 4.0 years ago by 41k • written 4.0 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
4.0 years ago Michael Love 41k
0
votes
6
replies
1.1k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 4.1 years ago by • 0 • written 4.1 years ago by • 0
0
votes
3
replies
2.6k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 4.2 years ago by 41k • written 4.2 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 41k • written 4.3 years ago by • 0
0
votes
5
replies
1.9k
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 41k • written 4.3 years ago by • 0
0
votes
5
replies
1.3k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
4.3 years ago omid.alamdari • 0
2
votes
11
replies
3.0k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
4.5 years ago • updated 4.4 years ago mico • 0
1
vote
3
replies
858
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
2.8k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.6 years ago k1m ▴ 20
1
vote
2
replies
924
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 4.6 years ago by 41k • written 4.6 years ago by ▴ 10
2
votes
3
replies
1.3k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 4.6 years ago by 41k • written 4.6 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 65k • written 4.7 years ago by • 0
1
vote
1
reply
968
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
4.7 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
4.8k
views
tximport transcript missing
deseq2 salmon tximport
4.8 years ago mr6518849 ▴ 10
0
votes
2
replies
935
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
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
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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