Showing : Tximport • reset
3
votes
4
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2.4k
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 3.0 years ago by ★ 4.9k • written 3.0 years ago by • 0
0
votes
3
replies
1.5k
views
tximport error
error tximport
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
5
votes
6
replies
2.4k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 3.0 years ago by 52k • written 3.0 years ago by • 0
0
votes
4
replies
1.8k
views
Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3.2 years ago uhlkatie • 0
1
vote
3
replies
2.9k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
votes
8
replies
2.4k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.2 years ago Kelen ▴ 10
0
votes
1
reply
1.6k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 3.3 years ago by ★ 4.9k • written 3.3 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
2
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3
replies
1.8k
views
Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3.3 years ago Maka • 0
6
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4
replies
4.2k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
3.4 years ago Al90 ▴ 10
0
votes
2
replies
3.3k
views
tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
3.5 years ago nakane_clan • 0
2
votes
5
replies
2.5k
views
from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
3.5 years ago Marianna ▴ 20
2
votes
3
replies
1.4k
views
Import RSEM output without sample data
DESeq2 tximportData tximport
updated 3.5 years ago by 43k • written 3.6 years ago by • 0
0
votes
1
reply
1.0k
views
tximport
salmon tximport
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
1
reply
1.3k
views
Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.7 years ago by ★ 4.9k • written 3.7 years ago by • 0
0
votes
3
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1.8k
views
tximport question on what counts to use for LogFC calculations
tximport
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
4
replies
2.2k
views
Filtering output from tximport
tximport Salmon
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
1
reply
1.8k
views
tximport samples with separate tx2gene maps
tximport
updated 3.8 years ago by 43k • written 3.9 years ago by • 0
1
vote
5
replies
3.9k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 2.1 years ago by 43k • written 3.8 years ago by • 0
2
votes
1
reply
2.6k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
votes
2
replies
2.1k
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 4.0 years ago by 43k • written 4.0 years ago by • 0
1
vote
2
replies
1.9k
views
tximeta countsFromAbundance for downstream analysis
tximeta tximport
4.1 years ago paulimer • 0
2
votes
3
replies
1.6k
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 50
2
votes
2
replies
1.8k
views
Issues with Tximport
tximport
4.2 years ago bryce.thomas • 0
0
votes
4
replies
2.8k
views
Tximport error message - colnames
tximport
written 4.2 years ago by • 0
0
votes
5
replies
1.7k
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 4.2 years ago by 43k • written 4.3 years ago by • 0
4
votes
3
replies
2.0k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 40
0
votes
1
reply
1.2k
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
6
replies
1.7k
views
Problem with Tximport to DESeq2
TxDb.Mmusculus.UCSC.mm10.ensGene DESeq2 tximport
4.3 years ago zli1 • 0
2
votes
2
replies
1.4k
views
TxImport when quant.sf files have different index files
tximport DESeq2
4.5 years ago mprnl • 0
3
votes
1
reply
1.5k
views
tximport rowsum error
tximport
4.5 years ago Ezgi ▴ 60
0
votes
1
reply
3.2k
views
DESeq2, tximport normalization, normalization factors, size factors
tximport DESeq2 normalizationfactors sizefactors
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
2
replies
1.1k
views
Pair-wise DESeq2 using tximport (running time and multi-threading)
tximport DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
vote
2
replies
3.1k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
4.5 years ago Nikolay Ivanov • 0
2
votes
2
replies
6.2k
views
Importing data into the DESeq2 pipeline using tximport
DESeq2 tximport
4.5 years ago Nikolay Ivanov • 0
0
votes
2
replies
1.3k
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
0
votes
7
replies
2.3k
views
Problem with Tximport
tximportData tximport
4.6 years ago agoesmartini • 0
0
votes
1
reply
1.3k
views
tximport error importing expected counts file from RSEM
RSEM tximport
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
2
votes
1
reply
2.3k
views
DESeq usage of transcript TPM after tximport
tximport
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
2
votes
1
reply
1.4k
views
tximport with salmon bootstraps and edger/deseq2
tximport
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
0
votes
5
replies
1.4k
views
sumarizeToGene is dropping transcripts, how to debug
sumarizeToGene tximport
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
6
votes
6
replies
3.0k
views
Transformation of raw RSEM gene expression estimates with variance stabilizing transformation and tximport R package
DESeq2 VST rsem tximport
4.8 years ago svlachavas ▴ 840
0
votes
1
reply
1.3k
views
How to use tx import on output of abundance file
tximportData tximport
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
1
vote
4
replies
1.5k
views
tximport abundanceCol parameter not functioning for rsem data
tximport rsem transcript abundance TPM FPKM
updated 4.8 years ago by 43k • written 5.0 years ago by • 0
1
vote
1
reply
2.7k
views
importing RSEM data into DESeq2
deseq2 tximport
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 10
1
vote
9
replies
2.1k
views
Question: Error running summarizeToGene() - RNA Seq Bioconductor pipeline
tximeta tximport deseq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 20
0
votes
8
replies
2.6k
views
Importing RSEM with tximport
tximport RSEM import error
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 60
2
votes
8
replies
5.2k
views
Which R version is needed for tximport package?
tximport package R version install tximport
5.0 years ago harelarik ▴ 60
0
votes
5
replies
2.0k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
votes
2
replies
1.4k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 20
297 results • Page 2 of 6
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Replies
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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