Showing : txImport • reset
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tximport allfile.exists(files)--> FALSE
tximport
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
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2
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734
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tximport latest version on bioconductor and bioconda
tximport
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
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1
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607
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Tximport Input file
tximport
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
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1
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1.2k
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Using tximport on RSEM abundance date
rnaseq rsem tximport
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
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4
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1.7k
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 50
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5
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1.9k
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countsFromAbundance for gene-level RSEM import in tximport
tximport rsem
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
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9
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1.8k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 20
2
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6
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2.2k
views
[DESeq2] Different results from tutorial
deseq2 tximportdata tximport
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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8
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3.3k
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Differences in gene length passed to DESeq2 by tximport reulted in different gene rankings
deseq2 tximport rsem saimon
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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3
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5.2k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 7.4 years ago by ★ 2.1k • written 7.4 years ago by ▴ 30
2
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3
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2.1k
views
how to get the lastest version of tximport
tximport stringtie
7.7 years ago • updated 7.5 years ago matrs ▴ 10
1
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5
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3.9k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 7.5 years ago by 43k • written 8.4 years ago by • 0
0
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1
reply
15k
views
there is no "tx2gene.gencode.v27.csv" in tximportData
tximport
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
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4
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4.2k
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Importing multiple .h5 files using tximport
Tutorial tximport
updated 6 weeks ago by 43k • written 7.5 years ago by ▴ 10
1
vote
1
reply
1.2k
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Post-processing RNA-Seq after tximport
salmon rna seq tximport ruv-seq deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
32
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16
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21k
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 7.5 years ago by ▴ 20 • written 9.3 years ago by ▴ 200
1
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4
replies
2.8k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 120
4
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3
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2.2k
views
Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2 tximport org.mm.eg.db gencode
7.6 years ago pvd2107 ▴ 30
2
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18
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4.3k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.6 years ago stephan.emmrich ▴ 10
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3
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1.8k
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Collapsing transcript counts into pathways / gene lists with DESeq2
deseq2 pathway analysis tximport
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
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1
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1.1k
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filtering lowly expressed genes before or after normalization?
edgeR TXIMPORT
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
2
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6
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2.6k
views
Can Tximport average transcript length be used for GOSeq?
deseq2 tximport goseq
7.6 years ago casey.rimland ▴ 170
1
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4
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3.2k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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1
reply
1.1k
views
tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
2
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6
replies
4.0k
views
Subsetting a tximport object
tximport
written 7.6 years ago by • 0
1
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2
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3.3k
views
use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
2
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2
replies
1.5k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
5
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10
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14k
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Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 30
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2
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1.2k
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Support site search not finding posts?
search tximport limma-trend
updated 7.7 years ago by 68k • written 7.7 years ago by ★ 2.0k
4
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3
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1.4k
views
Trouble with Tximport for edgeR
tximport edger
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
3
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13
replies
3.4k
views
tximport's parameter for countsFromAbundance doesn't work
tximport rsem edger
7.7 years ago tim.ivanov.92 • 0
5
votes
9
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4.2k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
7.7 years ago emmak ▴ 20
0
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1
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1.4k
views
Error with tximport on Kallisto .h5 data.
tximport kallisto bioconductor rnaseq
7.8 years ago srdjan.kasapovic0 • 0
1
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2
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1.2k
views
RNAseq tximport Deseq2
deseq2 tximport
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 30
2
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4
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3.2k
views
tximport of kallisto files
tximport deseq2 kallisto
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
3
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4
replies
4.6k
views
Importing RSEM transcript-level data using tximport
tximport rsem
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
2
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2
replies
2.4k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
2
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19
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3.4k
views
tximport returns NA counts
tximport
7.9 years ago leonfodoulian • 0
4
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5
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2.3k
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GAGE after tximport
gage tximport
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by ▴ 230
0
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3
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1.1k
views
RNA seq tximport
tximport
8.0 years ago tanyabioinfo ▴ 30
2
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4
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2.5k
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tximport gene name
tximport
updated 8.0 years ago by ▴ 230 • written 8.0 years ago by ▴ 30
1
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3
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5.6k
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PCA from TPM
pca tpm tximport
8.0 years ago tanyabioinfo ▴ 30
0
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3
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1.4k
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RNA seq tximport
tximport
8.0 years ago tanyabioinfo ▴ 30
3
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2
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2.0k
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tximport with versioned identifiers
tximport ensembldb
8.0 years ago Ed Siefker ▴ 230
3
votes
3
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1.8k
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Kallisto with tximport gives different results with asymmetrical experimental design
kallisto deseq2 tximport
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
1
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11
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8.5k
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RNA Seq data analysis using Salmon and tximport
RNAseq tximport
8.1 years ago tanyabioinfo ▴ 30
3
votes
5
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2.8k
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DESeqDataSetFromTximport with kallisto abundances.
deseq2 tximport
updated 8.1 years ago by • 0 • written 8.4 years ago by ▴ 30
0
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4
replies
3.2k
views
RangedSummarizedExperiment in Deseq2 and DESeqDataSetFromMatrix
rangedsummarizedexperiment deseqdatasetfrommatrix deseq2 tximport
8.1 years ago lirongrossmann ▴ 80
4
votes
9
replies
3.1k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ★ 2.0k
2
votes
4
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1.6k
views
Error in tximport, unused argument (reader = read_tsv)
tximport deseq2
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
297 results • Page 5 of 6
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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…
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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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