Showing : txImport • reset
8
votes
12
replies
4.9k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 8.1 years ago by ★ 2.1k • written 8.1 years ago by • 0
2
votes
7
replies
2.8k
views
Obtaining transcript names in RSEM
tximport rsem
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 20
1
vote
4
replies
1.9k
views
Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
salmon tximport limma-voom
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 30
0
votes
1
reply
940
views
Problem on tximport kallisto
tximport
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 40
2
votes
9
replies
2.6k
views
Unused argument of reader = read_tsv on R version 3.4.1
tximport
8.2 years ago tarun2 • 0
0
votes
4
replies
1.8k
views
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
8.2 years ago bruno.saubamea • 0
0
votes
1
reply
2.2k
views
confusion with tximport options and resulting matrix
tximport rnaseq rsem limma voom
updated 8.3 years ago by 53k • written 8.3 years ago by • 0
1
vote
5
replies
2.6k
views
tximport error with salmon version
deseq2 salmon tximport
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
4
votes
3
replies
4.1k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 3.8 years ago by • 0 • written 8.3 years ago by • 0
0
votes
1
reply
1.0k
views
how to deal with the cufflinks files
tximport
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
4
votes
9
replies
5.5k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 2.4 years ago by • 0 • written 8.3 years ago by • 0
0
votes
6
replies
2.4k
views
Different results obtained from mroast and camera from Deseq2 counts
limma camera mroast tximport
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 40
1
vote
0
replies
2.5k
views
How to test or estimate differential TSS/promoter usage/expression based on RNA-seq data only
tximport differential isoform usage salmon tss rna-seq
8.3 years ago Steffen Heyne ▴ 10
2
votes
3
replies
3.2k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
2
votes
2
replies
2.4k
views
tximport error: TXNAME from Txdb.mm10 and kallisto target_id mismatch
tximport kallisto txdb.mmusculus.ucsc.mm10.knowngene
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
0
votes
3
replies
2.4k
views
(very) conflicting results with DESeq2 between versions
deseq2 tximport rnaseq kallisto R
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
0
votes
6
replies
3.5k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
8.4 years ago sunil.mangalam • 0
0
votes
7
replies
3.1k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 4.0 years ago by • 0 • written 8.4 years ago by ▴ 40
2
votes
2
replies
1.3k
views
check splice isoforms
DESeq2 tximport
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
2
votes
5
replies
4.3k
views
unable to get tximport to work on data from kallisto
tximport kallisto
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 10
7
votes
17
replies
6.7k
views
DESeqDataSetFromTximport: Error in checkSlotAssignment
deseq2 tximport
8.5 years ago JWCarlson ▴ 80
1
vote
5
replies
3.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 70
6
votes
4
replies
5.8k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 10
1
vote
4
replies
2.6k
views
tximport error reading salmon quantification files...
tximport salmon
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 20
2
votes
7
replies
3.4k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
3
votes
5
replies
3.2k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 4.8 years ago by 68k • written 8.6 years ago by • 0
9
votes
4
replies
4.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 30
9
votes
11
replies
6.3k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.7 years ago by ▴ 20 • written 9.5 years ago by ▴ 10
9
votes
2
replies
11k
views
Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 4.1 years ago by 43k • written 8.7 years ago by ▴ 10
1
vote
1
reply
2.1k
views
How to remove genes with 0 counts in tximport?
tximport deseq tximportdata deseq2
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 20
0
votes
4
replies
1.8k
views
tximport RSEM error
tximport
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 100
2
votes
2
replies
1.4k
views
RNA-seq analysis without replicates using tximport and DESeq2
rnaseq deseq2 tximport
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 70
0
votes
6
replies
1.8k
views
Using tximport to read in data from sailfish experiment
tximport sailfish rnaseq
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
0
votes
4
replies
1.2k
views
Summarizing counts of alternate sequences in GRCh38
deseq2 tximport
9.0 years ago Chakravarthi Kanduri • 0
3
votes
2
replies
7.9k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 9.0 years ago by 43k • written 9.0 years ago by ★ 2.0k
1
vote
5
replies
2.3k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
0
votes
5
replies
11k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 19 months ago by • 0 • written 9.1 years ago by • 0
5
votes
5
replies
3.7k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 9.1 years ago by 43k • written 9.1 years ago by ★ 2.0k
2
votes
4
replies
2.4k
views
Any trick to use "tximport" for converting a simple read count table ?
tximport
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
1
vote
5
replies
1.8k
views
Help inputing sailfish TPM files into tximport
tximport sailfish
9.3 years ago sjmonkley ▴ 40
4
votes
3
replies
4.6k
views
txtimportData installation on R version 3.3.0 (2016-05-03)
tximport deseq2
9.3 years ago jarod_v6@libero.it ▴ 40
1
vote
3
replies
1.6k
views
Bias correction in single end experiment for DEG and DET
tximport alpine
9.4 years ago yohann.nedelec • 0
3
votes
1
reply
3.1k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 9.4 years ago by 43k • written 9.4 years ago by ★ 13k
4
votes
14
replies
3.5k
views
running tximport for salmon quants
tximport readr
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
3
votes
11
replies
3.3k
views
should I use rsem's summary to genes or tximport's?
tximport
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 10
1
vote
3
replies
2.4k
views
DESeq2 size factors estimation after RSEM quantification
deseq2 tximport rsem estimatesizefactors
9.5 years ago Hugo Varet ▴ 80
5
votes
9
replies
6.4k
views
Trouble with Tximport
tximport salmon
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 30
297 results • Page 6 of 6
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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