Showing : Salmon • reset
1
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218
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IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 7 weeks ago by ▴ 120 • written 8 weeks ago by ▴ 10
0
votes
3
replies
365
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 3 months ago by 40k • written 3 months ago by • 0
3
votes
12
replies
762
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Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 5 months ago by 40k • written 5 months ago by ▴ 10
0
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2
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417
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combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
3
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5
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750
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Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
7 months ago mohammedtoufiq91 ▴ 10
0
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2
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479
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how to match salmon output to txname
GenomicFeatures tximport salmon
written 8 months ago by • 0
0
votes
1
reply
386
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Missing transcript
DESeq2 tximport salmon
updated 8 months ago by ★ 3.4k • written 8 months ago by • 0
2
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1
reply
391
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Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 8 months ago by ★ 3.4k • written 8 months ago by • 0
2
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2
replies
630
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
written 9 months ago by • 0
0
votes
1
reply
535
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 10 months ago by ★ 3.4k • written 10 months ago by • 0
0
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2
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507
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dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
11 months ago manduchi ▴ 10
4
votes
1
reply
606
views
Adding custom transcript to Salmon index
salmon
updated 13 months ago by ★ 3.4k • written 13 months ago by ▴ 20
1
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3
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954
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 19 months ago by 40k • written 19 months ago by • 0
0
votes
1
reply
536
views
tximport
salmon tximport
updated 19 months ago by 40k • written 19 months ago by • 0
1
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1
reply
1.8k
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TPM to raw counts
salmon DESeq2
updated 20 months ago by 13k • written 20 months ago by • 0
0
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4
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1.2k
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Filtering output from tximport
tximport Salmon
updated 22 months ago by 40k • written 22 months ago by • 0
2
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2
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1.4k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
2.0 years ago Qin ▴ 10
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2
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1.0k
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 2.1 years ago by 40k • written 2.1 years ago by • 0
0
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14
replies
1.8k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
2.2 years ago • updated 2.1 years ago Abhishek • 0
2
votes
6
replies
3.7k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.3 years ago reganhayward • 0
2
votes
1
reply
809
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 2.3 years ago by 40k • written 2.4 years ago by • 0
1
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2
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1.5k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
2.6 years ago Nikolay Ivanov • 0
0
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7
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1.5k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 2.3 years ago by 40k • written 2.6 years ago by ▴ 20
0
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2
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705
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tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 2.6 years ago by 63k • written 2.6 years ago by • 0
0
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5
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1.2k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.1 years ago by 40k • written 3.1 years ago by • 0
2
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1
reply
1.2k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 3.1 years ago by 40k • written 3.1 years ago by ▴ 20
2
votes
2
replies
813
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.2 years ago keremwai • 0
2
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3
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681
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
0
votes
3
replies
938
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
1
vote
3
replies
1.2k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 3.4 years ago by 40k • written 3.4 years ago by ▴ 10
0
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4
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813
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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 3.4 years ago by 40k • written 3.4 years ago by • 0
4
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0
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1.6k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
3.4 years ago Michael Love 40k
0
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6
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830
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tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
0
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3
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2.1k
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 3.6 years ago by 40k • written 3.6 years ago by • 0
0
votes
1
reply
857
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 3.6 years ago by 40k • written 3.6 years ago by • 0
0
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5
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1.4k
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 3.7 years ago by 40k • written 3.7 years ago by • 0
0
votes
5
replies
910
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
3.7 years ago omid.alamdari • 0
2
votes
11
replies
2.4k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
3.9 years ago • updated 3.8 years ago mico • 0
1
vote
3
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614
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RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 3.9 years ago by 3.8k • written 3.9 years ago by ▴ 10
1
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8
replies
2.4k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.0 years ago k1m ▴ 20
1
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2
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691
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Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 4.0 years ago by 40k • written 4.0 years ago by ▴ 10
2
votes
3
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979
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 4.0 years ago by 40k • written 4.0 years ago by • 0
2
votes
7
replies
1.5k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 4.1 years ago by 63k • written 4.1 years ago by • 0
1
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1
reply
738
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
4.1 years ago konstantinos.bogias ▴ 10
5
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5
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4.2k
views
tximport transcript missing
deseq2 salmon tximport
4.2 years ago mr6518849 ▴ 10
0
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2
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683
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 4.3 years ago by 40k • written 4.3 years ago by ▴ 30
1
vote
3
replies
893
views
DESeq2 gives weird results
deseq2 salmon
updated 4.3 years ago by 40k • written 4.3 years ago by • 0
1
vote
1
reply
1.1k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 4.4 years ago by 40k • written 4.7 years ago by ▴ 60
1
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9
replies
2.0k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 4.5 years ago by ▴ 120 • written 4.5 years ago by • 0
14
votes
25
replies
2.2k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 4.5 years ago by ▴ 60
50 results • Page 1 of 1
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Comment: DMRcate design by James W. MacDonald 63k
That's what identical context means.
Comment: DMRcate design by Jitendra ▴ 10
Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?
Comment: Steps needed to change design (relevel factors) in DESeq2 by jd774 • 0
Thanks for the example code, would the `"condition_1_vs_2"` and `"condition_2_vs_1"` giving same or different results on DEGs and normalize…
Answer: heatmap.2 - change column & row locations; angle / rotate by nehagoyal6397 • 0
Window 10 are comes with the new updates [how to fix connections to wireless displays in windows 10](http://fixwindows10connections.com) ju…
Comment: filtering out lowly expressed genes by groups by James W. MacDonald 63k
You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…
Votes
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
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