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 20 days ago by ★ 4.6k • written 4 weeks ago by ▴ 10
4
votes
5
replies
645
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
7 weeks ago LuciaNhu • 0
0
votes
4
replies
606
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
6 months ago JG13 • 0
0
votes
3
replies
617
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
817
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 14 months ago by 43k • written 14 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
928
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 18 months ago by 43k • written 18 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 20 months ago by 43k • written 20 months ago by ▴ 10
0
votes
2
replies
1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
6
votes
10
replies
2.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 8 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 24 months ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 24 months ago by ★ 4.6k • written 24 months ago by • 0
2
votes
1
reply
998
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 24 months ago by ★ 4.6k • written 24 months 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 2.0 years ago by • 0
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.1 years ago by ★ 4.6k • written 2.1 years ago by • 0
0
votes
2
replies
1.4k
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
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
865
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 3.1 years ago by 43k • written 3.1 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
2.8k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
3.4 years ago Abhishek • 0
2
votes
6
replies
5.4k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.5 years ago reganhayward • 0
2
votes
1
reply
1.2k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
vote
2
replies
2.6k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
3.8 years ago Nikolay Ivanov • 0
0
votes
7
replies
2.5k
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 3.9 years ago by 67k • written 3.9 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 4.4 years ago by 43k • written 4.4 years ago by ▴ 20
2
votes
2
replies
1.3k
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 4.6 years ago by 43k • written 4.6 years ago by ▴ 10
0
votes
4
replies
1.4k
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
2.4k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.7 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 4.9 years ago by 43k • written 4.9 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 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
5
replies
1.5k
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
5.1 years ago mico • 0
1
vote
3
replies
1.1k
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
1.5k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
7
replies
2.3k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 5.3 years ago by 67k • written 5.3 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
5.4 years ago mr6518849 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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