Showing : salmon • reset
6
votes
10
replies
2.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
4
votes
5
replies
871
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
4 months ago LuciaNhu • 0
0
votes
4
replies
708
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
9 months ago JG13 • 0
0
votes
3
replies
719
views
Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
3
replies
965
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 17 months ago by 43k • written 17 months ago by • 0
1
vote
2
replies
2.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 20 months ago by ▴ 120 • written 20 months ago by ▴ 10
0
votes
3
replies
997
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 21 months ago by 43k • written 21 months ago by • 0
3
votes
12
replies
2.3k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 23 months ago by 43k • written 23 months ago by ▴ 10
0
votes
2
replies
1.5k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by • 0
6
votes
10
replies
3.2k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 11 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.3k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.2 years ago by • 0
0
votes
1
reply
1.2k
views
Missing transcript
DESeq2 tximport salmon
updated 2.2 years ago by ★ 4.7k • written 2.2 years ago by • 0
2
votes
1
reply
1.1k
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 2.2 years ago by ★ 4.7k • written 2.2 years ago by • 0
2
votes
5
replies
2.2k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 13 months ago by 43k • written 2.2 years ago by • 0
0
votes
1
reply
1.3k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.3 years ago by ★ 4.7k • written 2.3 years ago by • 0
0
votes
2
replies
1.6k
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
2.4 years ago manduchi ▴ 10
4
votes
1
reply
1.8k
views
Adding custom transcript to Salmon index
salmon
updated 2.6 years ago by ★ 4.7k • written 2.6 years ago by ▴ 20
1
vote
3
replies
1.9k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
votes
1
reply
919
views
tximport
salmon tximport
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
vote
2
replies
4.2k
views
TPM to raw counts
salmon DESeq2
updated 16 months ago by • 0 • written 3.2 years ago by • 0
0
votes
4
replies
2.0k
views
Filtering output from tximport
tximport Salmon
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
2
votes
2
replies
2.8k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
3.5 years ago Qin ▴ 10
0
votes
2
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1.9k
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 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
14
replies
3.1k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
3.7 years ago • updated 3.6 years ago Abhishek • 0
2
votes
6
replies
5.7k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.8 years ago reganhayward • 0
2
votes
1
reply
1.3k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 3.8 years ago by 43k • written 3.9 years ago by • 0
1
vote
2
replies
2.9k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
4.1 years ago Nikolay Ivanov • 0
0
votes
7
replies
2.8k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 3.8 years ago by 43k • written 4.1 years ago by ▴ 30
0
votes
2
replies
1.2k
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
0
votes
5
replies
1.9k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
2
votes
1
reply
1.9k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
4.7 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 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
3
replies
1.9k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
1
vote
3
replies
2.0k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 10
0
votes
4
replies
1.6k
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 4.9 years ago by 43k • written 4.9 years ago by • 0
4
votes
0
replies
2.6k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.9 years ago Michael Love 43k
0
votes
6
replies
1.4k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 5.0 years ago by • 0 • written 5.0 years ago by • 0
0
votes
3
replies
3.1k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
1
reply
1.4k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
5
replies
2.5k
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 5.2 years ago by 43k • written 5.2 years ago by • 0
0
votes
5
replies
1.7k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.2 years ago omid.alamdari • 0
2
votes
11
replies
3.7k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.4 years ago • updated 5.3 years ago mico • 0
1
vote
3
replies
1.3k
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by ▴ 10
1
vote
8
replies
3.6k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
5.5 years ago k1m ▴ 20
1
vote
2
replies
1.3k
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 10
2
votes
3
replies
1.7k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
2
votes
7
replies
2.5k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
1
vote
1
reply
1.3k
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
5.6 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
5.8k
views
tximport transcript missing
deseq2 salmon tximport
5.7 years ago mr6518849 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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