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kristoffer.vittingseerup ♦ 1.8k
Status: New
Handle: @kristoffer.vittingseerup17025
Reputation: 1800
Email: k*********@bio.ku.dk
Joined: 16 months ago
Twitter: @kvittingseerup
Last seen: 24 months ago
Location: European Union

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Answer: A: denovo transcriptome assembly
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Analysis rMATS of RNA Seq data
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.3k
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Comment: C: Alternative splicing analysis following kallisto?
16 months ago
kristoffer.vittingseerup ♦ 1.8k
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195
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Answer: A: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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269
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Comment: C: What is the most suitable normalisation technique for RNASeq data?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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159
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Answer: A: Analysis rMATS of RNA Seq data
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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159
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Comment: C: Analysis rMATS of RNA Seq data
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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122
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Comment: C: Salmon quasi Index upgrade
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: A: de novo assembly of raw illumina reads of RNA seq experiment (24gb data)
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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195
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Comment: C: Can I convert from PSI to RPKM?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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195
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Comment: C: Can I convert from PSI to RPKM?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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195
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Answer: A: Can I convert from PSI to RPKM?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: How to group gene dataset and run t.test for each row for every gene in R?
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: trim data with trimmomatic
17 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: SpliceJumper installation issues. Particularly with make
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.0k
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Comment: C: SpliceJumper installation issues. Particularly with make
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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168
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Comment: C: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Stringtie: use htseq-count or prepDE.py to extract reads?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: FastQC results interpretation
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: How to find SSR location i.e whether it is in CDS, or UTR
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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210
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Comment: C: Transcriptome analysis between two sample.
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Can we directly use batch corrected gene expression (Bulk RNA-seq) for further d
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Mean-variance trend in voom
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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348
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Comment: C: General question about batch effect, read trimming and what to do when the adapt
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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225
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Answer: A: Robust RNA-seq normalization
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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498
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Comment: C: How to make a plot with gProfileR results?
18 months ago
kristoffer.vittingseerup ♦ 1.8k
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324
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Comment: C: [rMATS] Number of AS Events from one sample
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: [rMATS] Number of AS Events from one sample
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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324
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Comment: C: [rMATS] Number of AS Events from one sample
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: TopHat error: IOError [errno 2] No such file or directory: '-o'
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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324
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Answer: A: [rMATS] Number of AS Events from one sample
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: [rMATS] Number of AS Events from one sample
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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202
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Answer: A: ADVOCATE R package
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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202
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Comment: C: ADVOCATE R package
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: how to deal with batch effect in TCGA RNA-seq dataset
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.6k
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Comment: C: Tools To Do the Alternative Splicing Analysis
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: rowVars function, used in ballgown analysis not available for R 3.5.2, alternati
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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298
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Answer: A: When exactly is a gene "expressed"?
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Cufflinks transcriptome (To build or not to build?)
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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198
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Comment: C: Cufflinks transcriptome (To build or not to build?)
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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442
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Answer: A: How to extract normalized matrix after using calcNormFact function (with TMM met
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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221
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Answer: A: Filtering values for two group separately
19 months ago
kristoffer.vittingseerup ♦ 1.8k
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123
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Sample level integration of two RNASeq datasets
RNA-Seq next-gen
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: download CNV file for breast cancer BRCA from TCGA website
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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414
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Comment: C: transcripts assemble by StringTie
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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414
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Answer: A: transcripts assemble by StringTie
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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205
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Answer: A: TPM normalization of transcript
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Get 3'UTR sequence using RNAseq read coverage
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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382
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Answer: A: Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Understanding FANTOM5 CAGE fields
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Understanding FANTOM5 CAGE fields
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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418
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Comment: C: How to create a summary statistics data table for omics data?
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Tools for prediction of protein functionality from AA sequence along
gene RNA-Seq Assembly
20 months ago
kristoffer.vittingseerup ♦ 1.8k • updated 20 months ago
Juke-34 ♦ 2.2k
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Answer: A: Splice site usage from RNA-seq data
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Is there a good way to get the proportions of isoforms *within* a condition usin
20 months ago
kristoffer.vittingseerup ♦ 1.8k
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272
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Answer: A: How to quantify mRNA transcripts from RNA-Seq data?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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351
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Comment: C: ANOVA or Linear regression for RNAseq data analysis with 3 factors
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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210
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Comment: C: Is there a good way to get the proportions of isoforms *within* a condition usin
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.6k
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Comment: C: Tools To Do the Alternative Splicing Analysis
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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1.6k
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Answer: A: Tools To Do the Alternative Splicing Analysis
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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292
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Answer: A: Given a list of cell surface genes, is there a computational possibility to pred
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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266
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Answer: A: Analyzing 3' RNA seq library with DEseq2
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Can I perform de novo analysis on RNA seq file of Mus musculus?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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222
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Answer: A: Percent abundance of two separate species in transcriptome data
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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257
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Answer: A: Can I perform de novo analysis on RNA seq file of Mus musculus?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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496
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Comment: C: How does monocle identify the begging of pseudotime?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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496
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Answer: A: How does monocle identify the begging of pseudotime?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: De novo transcriptome assembly produce too many transcripts
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Stringtie elimination of important transcripts
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Stringtie elimination of important transcripts
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Stringtie elimination of important transcripts
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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294
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Answer: A: Is it appropriate to apply RUVseq on output from kallisto?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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426
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Comment: C: Stringtie elimination of important transcripts
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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626
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Comment: C: What is RPKM/FPKM > 1 or 3 or 5?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: GETx patient RNA_Seq read count download
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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229
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Comment: C: GETx patient RNA_Seq read count download
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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517
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Comment: C: Is it fine to run SVM on RNA-seq read counts?
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: StringTie - Multimapped reads
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Differential expression: replicates in one condition, no replicates in the other
21 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Stringtie to DESeq2
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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459
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Comment: C: batch effect in RNAseq analysis using tophat cufflinks pipeline
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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459
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Answer: A: batch effect in RNAseq analysis using tophat cufflinks pipeline
22 months ago
kristoffer.vittingseerup ♦ 1.8k
1
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1
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1.1k
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Comment: C: How to see if adjusting batch effect in RNA-seq is working or not
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Novel protein isoform - how to investigate tissue and tissue expression using da
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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434
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Comment: C: scRNA-seq gene expression gradient onto tSNE plot
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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1.1k
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Comment: C: How to see if adjusting batch effect in RNA-seq is working or not
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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432
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Answer: A: How to change cellranger multimapping algorithm
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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297
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Comment: C: Sample-level differential expression for TCGA samples
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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485
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Comment: C: Extremely important marker gene has many reads based on IGV viewer but no quanti
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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Answer: A: Suggested pipelines for finding somatic mutations using RNAseq in normal and tum
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: Estimating individual batch factors
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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409
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Comment: C: How to deal with large inter-sample variation when using GTEx RNA-seq data?
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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409
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Comment: C: How to deal with large inter-sample variation when using GTEx RNA-seq data?
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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Comment: C: How to obtain mRNA splicing variants for a given chromosomal position?
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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266
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Answer: A: Identifiyng mutual trends between treatments
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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234
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Comment: C: How to perfectly use transcript merge method of various software like stringtie?
22 months ago
kristoffer.vittingseerup ♦ 1.8k
3
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1
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234
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Answer: A: How to perfectly use transcript merge method of various software like stringtie?
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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1
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266
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Comment: C: Identifiyng mutual trends between treatments
22 months ago
kristoffer.vittingseerup ♦ 1.8k
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