Showing : TXIMPORT • reset
4
votes
5
replies
567
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
19 days ago • updated 18 days ago LuciaNhu • 0
0
votes
2
replies
344
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
0
votes
2
replies
391
views
tximport data import
tximport
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
1
vote
2
replies
747
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
3 months ago grothmn • 0
1
vote
2
replies
2.2k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 5 months ago by ▴ 40 • written 5.1 years ago by • 0
0
votes
4
replies
572
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
5 months ago JG13 • 0
0
votes
2
replies
511
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
0
votes
2
replies
540
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 months ago by 43k • written 8 months ago by • 0
2
votes
1
reply
476
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 8 months ago by ★ 4.5k • written 8 months ago by • 0
2
votes
3
replies
2.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
0
votes
1
reply
670
views
tximport error with rsem files
rsem tximport
updated 11 months ago by ★ 4.5k • written 11 months ago by • 0
3
votes
2
replies
944
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 12 months ago by 67k • written 12 months ago by • 0
0
votes
3
replies
767
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 13 months ago by 43k • written 13 months ago by • 0
10
votes
11
replies
2.7k
views
tximport error: vroom
tximport
updated 13 months ago by • 0 • written 13 months ago by ▴ 40
2
votes
3
replies
1.2k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 15 months ago by • 0
4
votes
13
replies
2.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
0
votes
4
replies
1.4k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 15 months ago by 43k • written 15 months ago by • 0
1
vote
2
replies
2.2k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 16 months ago by ▴ 120 • written 16 months ago by ▴ 10
2
votes
9
replies
1.7k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
17 months ago • updated 16 months ago Ndimensional ▴ 20
0
votes
2
replies
904
views
tximport error in reading salmon output files?
tximport tximportData
updated 9 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
884
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 18 months ago by 67k • written 18 months ago by • 0
2
votes
1
reply
976
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 18 months ago by 43k • written 18 months ago by • 0
3
votes
7
replies
1.5k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
19 months ago • updated 18 months ago Yijing • 0
0
votes
2
replies
1.2k
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
19 months ago Yijing • 0
1
vote
3
replies
1.2k
views
tximport error
tximport r
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
2
replies
1.3k
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 21 months ago by ★ 4.5k • written 21 months ago by • 0
1
vote
5
replies
1.6k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 21 months ago by 43k • written 21 months ago by ▴ 90
6
votes
10
replies
2.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 months ago by • 0 • written 21 months ago by ▴ 10
0
votes
1
reply
945
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 22 months ago by ★ 1.5k • written 22 months ago by ▴ 10
0
votes
2
replies
1.1k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 22 months ago by • 0
0
votes
1
reply
1.1k
views
Missing transcript
DESeq2 tximport salmon
updated 22 months ago by ★ 4.5k • written 22 months ago by • 0
2
votes
1
reply
972
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 22 months ago by ★ 4.5k • written 23 months ago by • 0
2
votes
5
replies
1.9k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 months ago by 43k • written 23 months ago by • 0
0
votes
2
replies
1.0k
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
24 months ago Konstantinos • 0
2
votes
3
replies
1.6k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
24 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.4k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 2.0 years ago by 67k • written 2.0 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.0 years ago by ★ 4.5k • written 2.0 years ago by • 0
1
vote
2
replies
1.0k
views
error loading kallisto output in tximport
file.exists false kallisto tximport
2.0 years ago cta • 0
2
votes
3
replies
1.7k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.1 years ago by ▴ 50
3
votes
3
replies
1.3k
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
2.1 years ago duhwa.lee • 0
1
vote
2
replies
2.0k
views
transcripts missing from tx2gene
tximport
2.2 years ago Erick • 0
0
votes
1
reply
867
views
tximport: not all(file.exists(files)) are true
tximport
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
2
votes
1
reply
2.5k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by ▴ 10
3
votes
4
replies
1.8k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by • 0
0
votes
3
replies
1.2k
views
tximport error
error tximport
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
5
votes
6
replies
1.9k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
votes
4
replies
1.5k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
2.4 years ago uhlkatie • 0
1
vote
3
replies
2.2k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.4 years ago Kelen ▴ 10
0
votes
1
reply
1.3k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.5 years ago by ★ 4.5k • written 2.5 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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