Showing : Salmon • reset
0
votes
4
replies
314
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
12 days ago • updated 11 days ago JG13 • 0
0
votes
3
replies
362
views
Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 4 months ago by 42k • written 4 months ago by • 0
0
votes
3
replies
486
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 8 months ago by 42k • written 8 months ago by • 0
1
vote
2
replies
1.7k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 10 months ago by ▴ 120 • written 10 months ago by ▴ 10
0
votes
3
replies
746
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 12 months ago by 42k • written 12 months ago by • 0
3
votes
12
replies
1.6k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 14 months ago by 42k • written 14 months ago by ▴ 10
0
votes
2
replies
987
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
6
votes
10
replies
1.9k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 8 weeks ago by • 0 • written 16 months ago by ▴ 10
0
votes
2
replies
887
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 17 months ago by • 0
0
votes
1
reply
813
views
Missing transcript
DESeq2 tximport salmon
updated 17 months ago by ★ 4.2k • written 17 months ago by • 0
2
votes
1
reply
754
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 17 months ago by ★ 4.2k • written 17 months ago by • 0
2
votes
5
replies
1.5k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 3 months ago by 42k • written 17 months ago by • 0
0
votes
1
reply
953
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 19 months ago by ★ 4.2k • written 19 months ago by • 0
0
votes
2
replies
1.1k
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
20 months ago manduchi ▴ 10
4
votes
1
reply
1.1k
views
Adding custom transcript to Salmon index
salmon
updated 22 months ago by ★ 4.2k • written 22 months ago by ▴ 20
1
vote
3
replies
1.5k
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
743
views
tximport
salmon tximport
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
1
vote
2
replies
3.0k
views
TPM to raw counts
salmon DESeq2
updated 6 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 2.6 years ago by 42k • written 2.6 years ago by • 0
2
votes
2
replies
2.2k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
2.8 years ago • updated 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 2.8 years ago by 42k • written 2.8 years ago by • 0
0
votes
14
replies
2.4k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
2.9 years ago Abhishek • 0
2
votes
6
replies
4.7k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.0 years ago reganhayward • 0
2
votes
1
reply
1.1k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
1
vote
2
replies
2.2k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
3.3 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
973
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.4 years ago by 66k • written 3.4 years ago by • 0
0
votes
5
replies
1.5k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
2
votes
1
reply
1.6k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 3.9 years ago by 42k • written 3.9 years ago by ▴ 20
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
4.0 years ago keremwai • 0
2
votes
3
replies
959
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
1.4k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 4.1 years ago by 42k • written 4.1 years ago by • 0
1
vote
3
replies
1.6k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.1 years ago by 42k • written 4.1 years ago by ▴ 10
0
votes
4
replies
1.2k
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 4.2 years ago by 42k • written 4.2 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
4.2 years ago Michael Love 42k
0
votes
6
replies
1.2k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 4.2 years ago by • 0 • written 4.3 years ago by • 0
0
votes
3
replies
2.6k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
0
votes
1
reply
1.1k
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 4.4 years ago by 42k • written 4.4 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 4.4 years ago by 42k • written 4.4 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
4.6 years ago • updated 4.5 years ago mico • 0
1
vote
3
replies
913
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 4.6 years ago by ★ 3.9k • written 4.6 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
965
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 4.8 years ago by 42k • written 4.8 years ago by • 0
2
votes
7
replies
2.0k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 4.8 years ago by 66k • written 4.8 years ago by • 0
1
vote
1
reply
993
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
5.0k
views
tximport transcript missing
deseq2 salmon tximport
4.9 years ago mr6518849 ▴ 10
0
votes
2
replies
992
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 5.0 years ago by 42k • written 5.0 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
50 results • Page 1 of 1
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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