Showing : salmon • reset
6
votes
10
replies
2.5k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by ▴ 10
4
votes
5
replies
672
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 weeks ago • updated 9 weeks ago LuciaNhu • 0
0
votes
4
replies
623
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
7 months ago JG13 • 0
0
votes
3
replies
639
views
Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
3
replies
835
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
vote
2
replies
2.3k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 17 months ago by ▴ 120 • written 17 months ago by ▴ 10
0
votes
3
replies
939
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 19 months ago by 43k • written 19 months ago by • 0
3
votes
12
replies
2.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
0
votes
2
replies
1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
6
votes
10
replies
2.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 9 months ago by • 0 • written 23 months ago by ▴ 10
0
votes
2
replies
1.2k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
votes
1
reply
1.0k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
2
votes
5
replies
2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 months ago by 43k • written 2.1 years ago by • 0
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.2 years ago by ★ 4.6k • written 2.2 years ago by • 0
0
votes
2
replies
1.5k
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
2.3 years ago • updated 2.2 years ago manduchi ▴ 10
4
votes
1
reply
1.5k
views
Adding custom transcript to Salmon index
salmon
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by ▴ 20
1
vote
3
replies
1.8k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
869
views
tximport
salmon tximport
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
1
vote
2
replies
3.9k
views
TPM to raw counts
salmon DESeq2
updated 13 months ago by • 0 • written 3.0 years ago by • 0
0
votes
4
replies
1.9k
views
Filtering output from tximport
tximport Salmon
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
votes
2
replies
2.7k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
3.3 years ago Qin ▴ 10
0
votes
2
replies
1.8k
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 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
14
replies
2.9k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
3.5 years ago Abhishek • 0
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.6 years ago reganhayward • 0
2
votes
1
reply
1.2k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
2
replies
2.7k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
3.9 years ago Nikolay Ivanov • 0
0
votes
7
replies
2.6k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 3.6 years ago by 43k • written 3.9 years ago by ▴ 30
0
votes
2
replies
1.1k
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 4.0 years ago by 67k • written 4.0 years ago by • 0
0
votes
5
replies
1.8k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
2
votes
1
reply
1.8k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
4.5 years ago keremwai • 0
2
votes
3
replies
1.2k
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
0
votes
3
replies
1.7k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
vote
3
replies
1.8k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
0
votes
4
replies
1.5k
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 4.7 years ago by 43k • written 4.7 years ago by • 0
4
votes
0
replies
2.5k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.8 years ago Michael Love 43k
0
votes
6
replies
1.4k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 4.8 years ago by • 0 • written 4.8 years ago by • 0
0
votes
3
replies
3.0k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
1
reply
1.3k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
5
replies
2.4k
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 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
5
replies
1.6k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.0 years ago omid.alamdari • 0
2
votes
11
replies
3.5k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.2 years ago • updated 5.1 years ago mico • 0
1
vote
3
replies
1.2k
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 10
1
vote
8
replies
3.4k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
5.3 years ago k1m ▴ 20
1
vote
2
replies
1.2k
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 5.3 years ago by 43k • written 5.4 years ago by • 0
2
votes
7
replies
2.4k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 5.4 years ago by 67k • written 5.4 years ago by • 0
1
vote
1
reply
1.2k
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
5.4 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
5.6k
views
tximport transcript missing
deseq2 salmon tximport
5.5 years ago mr6518849 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
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