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kristoffer.vittingseerup ♦ 1.8k
Status: New
Handle: @kristoffer.vittingseerup17025
Reputation: 1800
Email: k*********@bio.ku.dk
Joined: 12 months ago
Twitter: @kvittingseerup
Last seen: 20 months ago
Location: European Union

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A: denovo transcriptome assembly
12 months ago
kristoffer.vittingseerup ♦ 1.8k
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C: Analysis rMATS of RNA Seq data
12 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.3k
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C: Alternative splicing analysis following kallisto?
12 months ago
kristoffer.vittingseerup ♦ 1.8k
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187
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A: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
13 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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264
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C: What is the most suitable normalisation technique for RNASeq data?
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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158
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A: Analysis rMATS of RNA Seq data
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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158
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C: Analysis rMATS of RNA Seq data
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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113
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C: Salmon quasi Index upgrade
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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208
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A: de novo assembly of raw illumina reads of RNA seq experiment (24gb data)
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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188
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C: Can I convert from PSI to RPKM?
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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188
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C: Can I convert from PSI to RPKM?
13 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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188
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A: Can I convert from PSI to RPKM?
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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135
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C: How to group gene dataset and run t.test for each row for every gene in R?
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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179
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A: trim data with trimmomatic
13 months ago
kristoffer.vittingseerup ♦ 1.8k
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167
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C: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.0k
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C: SpliceJumper installation issues. Particularly with make
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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1.0k
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C: SpliceJumper installation issues. Particularly with make
14 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
Reply
167
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C: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
14 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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0
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224
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A: Stringtie: use htseq-count or prepDE.py to extract reads?
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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241
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A: FastQC results interpretation
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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745
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C: How to find SSR location i.e whether it is in CDS, or UTR
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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206
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C: Transcriptome analysis between two sample.
14 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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121
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A: Can we directly use batch corrected gene expression (Bulk RNA-seq) for further d
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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204
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C: Mean-variance trend in voom
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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341
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C: General question about batch effect, read trimming and what to do when the adapt
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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224
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A: Robust RNA-seq normalization
14 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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490
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C: How to make a plot with gProfileR results?
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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320
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C: [rMATS] Number of AS Events from one sample
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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320
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C: [rMATS] Number of AS Events from one sample
15 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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320
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C: [rMATS] Number of AS Events from one sample
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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220
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A: TopHat error: IOError [errno 2] No such file or directory: '-o'
15 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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320
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A: [rMATS] Number of AS Events from one sample
15 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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320
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C: [rMATS] Number of AS Events from one sample
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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201
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A: ADVOCATE R package
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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201
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C: ADVOCATE R package
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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315
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A: how to deal with batch effect in TCGA RNA-seq dataset
15 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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1.6k
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C: Tools To Do the Alternative Splicing Analysis
15 months ago
kristoffer.vittingseerup ♦ 1.8k
4
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1
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335
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A: rowVars function, used in ballgown analysis not available for R 3.5.2, alternati
15 months ago
kristoffer.vittingseerup ♦ 1.8k
3
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1
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289
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A: When exactly is a gene "expressed"?
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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195
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C: Cufflinks transcriptome (To build or not to build?)
15 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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195
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C: Cufflinks transcriptome (To build or not to build?)
15 months ago
kristoffer.vittingseerup ♦ 1.8k
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439
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A: How to extract normalized matrix after using calcNormFact function (with TMM met
16 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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220
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A: Filtering values for two group separately
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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121
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Sample level integration of two RNASeq datasets
RNA-Seq next-gen
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.2k
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A: download CNV file for breast cancer BRCA from TCGA website
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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406
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C: transcripts assemble by StringTie
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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406
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A: transcripts assemble by StringTie
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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202
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A: TPM normalization of transcript
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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378
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C: Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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349
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A: Get 3'UTR sequence using RNAseq read coverage
16 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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378
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A: Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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242
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C: Understanding FANTOM5 CAGE fields
16 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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242
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A: Understanding FANTOM5 CAGE fields
16 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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411
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C: How to create a summary statistics data table for omics data?
16 months ago
kristoffer.vittingseerup ♦ 1.8k
3
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2
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218
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Tools for prediction of protein functionality from AA sequence along
gene RNA-Seq Assembly
16 months ago
kristoffer.vittingseerup ♦ 1.8k • updated 16 months ago
Juke-34 ♦ 2.2k
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310
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A: Splice site usage from RNA-seq data
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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208
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C: Is there a good way to get the proportions of isoforms *within* a condition usin
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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269
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A: How to quantify mRNA transcripts from RNA-Seq data?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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350
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C: ANOVA or Linear regression for RNAseq data analysis with 3 factors
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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208
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C: Is there a good way to get the proportions of isoforms *within* a condition usin
17 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
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1.6k
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C: Tools To Do the Alternative Splicing Analysis
17 months ago
kristoffer.vittingseerup ♦ 1.8k
4
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1
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1.6k
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A: Tools To Do the Alternative Splicing Analysis
17 months ago
kristoffer.vittingseerup ♦ 1.8k
3
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0
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289
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A: Given a list of cell surface genes, is there a computational possibility to pred
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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265
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A: Analyzing 3' RNA seq library with DEseq2
17 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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252
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C: Can I perform de novo analysis on RNA seq file of Mus musculus?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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220
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A: Percent abundance of two separate species in transcriptome data
17 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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252
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A: Can I perform de novo analysis on RNA seq file of Mus musculus?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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491
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C: How does monocle identify the begging of pseudotime?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
4
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1
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491
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A: How does monocle identify the begging of pseudotime?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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330
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C: De novo transcriptome assembly produce too many transcripts
17 months ago
kristoffer.vittingseerup ♦ 1.8k
2
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423
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C: Stringtie elimination of important transcripts
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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423
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C: Stringtie elimination of important transcripts
17 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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423
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C: Stringtie elimination of important transcripts
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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0
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292
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A: Is it appropriate to apply RUVseq on output from kallisto?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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423
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C: Stringtie elimination of important transcripts
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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622
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C: What is RPKM/FPKM > 1 or 3 or 5?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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228
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A: GETx patient RNA_Seq read count download
17 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
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228
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C: GETx patient RNA_Seq read count download
17 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
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513
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C: Is it fine to run SVM on RNA-seq read counts?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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0
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314
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A: StringTie - Multimapped reads
18 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1.1k
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A: Differential expression: replicates in one condition, no replicates in the other
18 months ago
kristoffer.vittingseerup ♦ 1.8k
3
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0
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3.4k
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A: Stringtie to DESeq2
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
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453
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C: batch effect in RNAseq analysis using tophat cufflinks pipeline
18 months ago
kristoffer.vittingseerup ♦ 1.8k
2
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0
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453
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A: batch effect in RNAseq analysis using tophat cufflinks pipeline
18 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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1.1k
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C: How to see if adjusting batch effect in RNA-seq is working or not
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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0
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402
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A: Novel protein isoform - how to investigate tissue and tissue expression using da
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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0
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433
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C: scRNA-seq gene expression gradient onto tSNE plot
18 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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1.1k
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C: How to see if adjusting batch effect in RNA-seq is working or not
18 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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0
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431
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A: How to change cellranger multimapping algorithm
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
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291
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C: Sample-level differential expression for TCGA samples
18 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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0
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482
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C: Extremely important marker gene has many reads based on IGV viewer but no quanti
18 months ago
kristoffer.vittingseerup ♦ 1.8k
2
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0
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897
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A: Suggested pipelines for finding somatic mutations using RNAseq in normal and tum
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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0
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188
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C: Estimating individual batch factors
18 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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404
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C: How to deal with large inter-sample variation when using GTEx RNA-seq data?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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404
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C: How to deal with large inter-sample variation when using GTEx RNA-seq data?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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0
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204
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C: How to obtain mRNA splicing variants for a given chromosomal position?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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0
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264
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A: Identifiyng mutual trends between treatments
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
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233
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C: How to perfectly use transcript merge method of various software like stringtie?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
3
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1
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233
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A: How to perfectly use transcript merge method of various software like stringtie?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
0
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1
Reply
264
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C: Identifiyng mutual trends between treatments
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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