Showing : txImport • reset
3
votes
2
replies
229
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 6 days ago by 64k • written 6 days ago by • 0
0
votes
3
replies
234
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
10
votes
11
replies
1.2k
views
tximport error: vroom
tximport
updated 5 weeks ago by • 0 • written 8 weeks ago by ▴ 40
2
votes
3
replies
477
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 3 months ago by • 0
4
votes
13
replies
762
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 9 weeks ago by 41k • written 3 months ago by • 0
0
votes
4
replies
473
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 3 months ago by 41k • written 3 months ago by • 0
1
vote
2
replies
564
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 4 months ago by ▴ 120 • written 4 months ago by ▴ 10
2
votes
9
replies
796
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
5 months ago • updated 4 months ago Ndimensional ▴ 20
0
votes
2
replies
415
views
tximport error in reading salmon output files?
tximport tximportData
5 months ago barrypraveen • 0
0
votes
1
reply
407
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 6 months ago by 64k • written 6 months ago by • 0
2
votes
1
reply
404
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 6 months ago by 41k • written 6 months ago by • 0
3
votes
7
replies
728
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
7 months ago • updated 6 months ago Yijing • 0
0
votes
2
replies
485
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
7 months ago Yijing • 0
1
vote
3
replies
552
views
tximport error
tximport r
updated 7 months ago by 41k • written 7 months ago by • 0
0
votes
2
replies
574
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 9 months ago by ★ 3.6k • written 9 months ago by • 0
1
vote
5
replies
848
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 9 months ago by 41k • written 9 months ago by ▴ 90
3
votes
5
replies
939
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
10 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
490
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 10 months ago by ★ 1.5k • written 10 months ago by ▴ 10
0
votes
2
replies
583
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 10 months ago by • 0
0
votes
1
reply
506
views
Missing transcript
DESeq2 tximport salmon
updated 11 months ago by ★ 3.6k • written 11 months ago by • 0
2
votes
1
reply
490
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 11 months ago by ★ 3.6k • written 11 months ago by • 0
2
votes
2
replies
826
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
written 11 months ago by • 0
0
votes
2
replies
578
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
12 months ago Konstantinos • 0
2
votes
3
replies
913
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
12 months ago mohammedtoufiq91 ▴ 10
4
votes
3
replies
751
views
tx2gene object trouble when working with kallisto and A.thaliana
tx2gene tximport Arabidopsis_thaliana kallisto
updated 12 months ago by 64k • written 12 months ago by ▴ 10
0
votes
1
reply
660
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 12 months ago by ★ 3.6k • written 12 months ago by • 0
1
vote
2
replies
589
views
error loading kallisto output in tximport
file.exists false kallisto tximport
13 months ago • updated 12 months ago cta • 0
2
votes
2
replies
908
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
13 months ago L ▴ 50
3
votes
3
replies
676
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
13 months ago duhwa.lee • 0
1
vote
2
replies
1.1k
views
transcripts missing from tx2gene
tximport
14 months ago Erick • 0
0
votes
1
reply
498
views
tximport: not all(file.exists(files)) are true
tximport
updated 14 months ago by 41k • written 14 months ago by • 0
2
votes
1
reply
1.1k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 14 months ago by ★ 3.6k • written 14 months ago by ▴ 10
3
votes
4
replies
822
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 14 months ago by ★ 3.6k • written 14 months ago by • 0
0
votes
3
replies
734
views
tximport error
error tximport
updated 14 months ago by 41k • written 15 months ago by • 0
5
votes
6
replies
1.1k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 14 months ago by 49k • written 15 months ago by • 0
0
votes
4
replies
865
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
17 months ago uhlkatie • 0
1
vote
3
replies
1.3k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 17 months ago by 41k • written 17 months ago by • 0
2
votes
8
replies
1.2k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
17 months ago Kelen ▴ 10
0
votes
1
reply
767
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 18 months ago by ★ 3.6k • written 18 months ago by ▴ 10
0
votes
1
reply
712
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 19 months ago by 41k • written 19 months ago by • 0
2
votes
3
replies
976
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
19 months ago Maka • 0
5
votes
4
replies
1.7k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
20 months ago Al90 ▴ 10
0
votes
2
replies
2.0k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
21 months ago nakane_clan • 0
2
votes
5
replies
1.5k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
21 months ago Marianna ▴ 10
2
votes
3
replies
803
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 21 months ago by 41k • written 22 months ago by • 0
0
votes
1
reply
604
views
tximport
salmon tximport
updated 22 months ago by 41k • written 22 months ago by • 0
0
votes
1
reply
738
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 23 months ago by ★ 3.6k • written 23 months ago by • 0
0
votes
3
replies
1.1k
views
tximport question on what counts to use for LogFC calculations
tximport
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
votes
4
replies
1.3k
views
Filtering output from tximport
tximport Salmon
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
tximport samples with separate tx2gene maps
tximport
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Yes. I considered genome wide p value as cutoff.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
It sounds like you have more overlaps than by chance, is that what you would like to see?
Comment: ATACseqQC shiftGAlignmentsList() problem by Ou, Jianhong ★ 1.3k
Hi, Thank you for trying ATACseqQC. Could you let me know the version of ATACseqQC you are using? And did you try to set `bigFile=TRUE` wh…
Answer: GENESIS: Can not use GdsGenotypeReader to read a gds file by Stephanie M. Gogarten ▴ 870
`SeqVarTools` and `GWASTools` provide two alternate paths to working with files in `GENESIS`, depending on what type of GDS file you start …
Answer: GENESIS: Can not use GdsGenotypeReader to read a gds file by James W. MacDonald 64k
If you can open the file using `seqOpen` you should not expect that you will be able to open using `GdsGenotypeReader`. ``` > library(S…
Votes
Attempting to import SBML file using R
Answer: RNASeq time course analysis, missing time points for control
Answer: biomaRt not working - lazy table error
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
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