Showing : txImport • reset
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 days ago by • 0 • written 14 months ago by ▴ 10
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
23 days ago Marianna ▴ 20
0
votes
2
replies
195
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 5 weeks ago by • 0 • written 7.6 years ago by • 0
2
votes
1
reply
236
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 weeks ago by 41k • written 16 months ago by • 0
0
votes
2
replies
646
views
tximport error in reading salmon output files?
tximport tximportData
updated 12 weeks ago by • 0 • written 10 months ago by • 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
0
votes
1
reply
326
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
3
votes
2
replies
550
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 6 months ago by ▴ 40
0
votes
3
replies
415
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 months ago by 41k • written 6 months ago by • 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
2
votes
3
replies
797
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
0
votes
4
replies
860
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
1
vote
2
replies
1.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 months ago by ▴ 120 • written 9 months ago by ▴ 10
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by 41k • written 2.5 years ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 0
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by ▴ 190 • written 3.8 years ago by ▴ 620
0
votes
1
reply
597
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
2
votes
1
reply
642
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago • updated 11 months ago Yijing • 0
0
votes
2
replies
816
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago Yijing • 0
1
vote
3
replies
853
views
tximport error
tximport r
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
2
replies
910
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 14 months ago by 41k • written 14 months ago by ▴ 90
0
votes
1
reply
715
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 15 months ago by ★ 1.5k • written 15 months ago by ▴ 10
0
votes
2
replies
787
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 15 months ago by • 0
0
votes
1
reply
730
views
Missing transcript
DESeq2 tximport salmon
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
2
votes
1
reply
666
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
0
votes
2
replies
777
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
17 months ago Konstantinos • 0
2
votes
3
replies
1.2k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
17 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
1.1k
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 17 months ago by 65k • written 17 months ago by ▴ 10
0
votes
4
replies
1.9k
views
Tximport error message - colnames
tximport
written 2.9 years ago by • 0
0
votes
1
reply
888
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
1
vote
2
replies
785
views
error loading kallisto output in tximport
file.exists false kallisto tximport
17 months ago cta • 0
3
votes
3
replies
918
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
18 months ago • updated 17 months ago duhwa.lee • 0
2
votes
2
replies
1.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
18 months ago L ▴ 50
1
vote
2
replies
1.5k
views
transcripts missing from tx2gene
tximport
19 months ago Erick • 0
0
votes
1
reply
627
views
tximport: not all(file.exists(files)) are true
tximport
updated 19 months ago by 41k • written 19 months ago by • 0
3
votes
4
replies
1.2k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
2
votes
1
reply
1.5k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 19 months ago by ★ 4.0k • written 19 months ago by ▴ 10
0
votes
3
replies
963
views
tximport error
error tximport
updated 19 months ago by 41k • written 19 months ago by • 0
5
votes
6
replies
1.4k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 19 months ago by 50k • written 20 months ago by • 0
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
22 months ago uhlkatie • 0
1
vote
3
replies
1.7k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 22 months ago by 41k • written 22 months ago by • 0
0
votes
1
reply
999
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 23 months ago by ★ 4.0k • written 23 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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