Showing : tximport • reset
0
votes
2
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203
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
0
votes
2
replies
225
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
2
votes
1
reply
276
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 10 weeks ago by ★ 4.2k • written 10 weeks ago by • 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
1
reply
377
views
tximport error with rsem files
rsem tximport
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
3
votes
2
replies
597
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 66k • written 5 months ago by • 0
0
votes
3
replies
459
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 7 months ago by 42k • written 7 months ago by • 0
10
votes
11
replies
2.0k
views
tximport error: vroom
tximport
updated 7 months ago by • 0 • written 7 months ago by ▴ 40
2
votes
3
replies
848
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
4
votes
13
replies
1.5k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 8 months ago by 42k • written 9 months ago by • 0
0
votes
4
replies
942
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 9 months ago by 42k • written 9 months ago by • 0
1
vote
2
replies
1.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 months ago by ▴ 120 • written 10 months ago by ▴ 10
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
0
votes
2
replies
695
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 11 months ago by • 0
0
votes
1
reply
655
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 12 months ago by 66k • written 12 months ago by • 0
2
votes
1
reply
685
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 12 months ago by 42k • written 12 months ago by • 0
3
votes
7
replies
1.2k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
0
votes
2
replies
867
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
13 months ago • updated 12 months ago Yijing • 0
1
vote
3
replies
907
views
tximport error
tximport r
updated 13 months ago by 42k • written 13 months ago by • 0
0
votes
2
replies
957
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
1
vote
5
replies
1.2k
views
tximport: kallisto + GENCODE transcript sanitization
tximport
updated 15 months ago by 42k • written 15 months ago by ▴ 90
6
votes
10
replies
1.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 5 weeks ago by • 0 • written 15 months ago by ▴ 10
0
votes
1
reply
763
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 16 months ago by ★ 1.5k • written 16 months ago by ▴ 10
0
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2
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842
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
votes
1
reply
780
views
Missing transcript
DESeq2 tximport salmon
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
2
votes
1
reply
719
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 3 months ago by 42k • written 17 months ago by • 0
0
votes
2
replies
809
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
18 months ago Konstantinos • 0
2
votes
3
replies
1.3k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
18 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 18 months ago by 66k • written 18 months ago by ▴ 10
0
votes
1
reply
921
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 18 months ago by ★ 4.2k • written 18 months ago by • 0
1
vote
2
replies
815
views
error loading kallisto output in tximport
file.exists false kallisto tximport
18 months ago cta • 0
2
votes
2
replies
1.3k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
19 months ago L ▴ 50
3
votes
3
replies
972
views
What is the correct way to import transcript abundances from 3' Quantseq results that calculated by kallisto?
tximport tximportData Quantseq kallisto
19 months ago • updated 18 months ago duhwa.lee • 0
1
vote
2
replies
1.6k
views
transcripts missing from tx2gene
tximport
20 months ago Erick • 0
0
votes
1
reply
655
views
tximport: not all(file.exists(files)) are true
tximport
updated 20 months ago by 42k • written 20 months ago by • 0
2
votes
1
reply
1.6k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 20 months ago by ★ 4.2k • written 20 months ago by ▴ 10
3
votes
4
replies
1.3k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 20 months ago by ★ 4.2k • written 20 months ago by • 0
0
votes
3
replies
999
views
tximport error
error tximport
updated 20 months ago by 42k • written 20 months ago by • 0
5
votes
6
replies
1.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 20 months ago by 50k • written 21 months ago by • 0
0
votes
4
replies
1.1k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
23 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 23 months ago by 42k • written 23 months ago by • 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
23 months ago Kelen ▴ 10
0
votes
1
reply
1.1k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.0 years ago by ★ 4.2k • written 2.0 years ago by ▴ 10
0
votes
1
reply
865
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 2.0 years ago by 42k • written 2.1 years ago by • 0
2
votes
3
replies
1.3k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
2.1 years ago Maka • 0
6
votes
4
replies
2.4k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
2.1 years ago Al90 ▴ 10
0
votes
2
replies
2.5k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
2.2 years ago nakane_clan • 0
2
votes
5
replies
1.8k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
2.3 years ago Marianna ▴ 20
2
votes
3
replies
976
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
50 results • Page 1 of 1
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Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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