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2
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Batch correct batch 2 while leaving batch 1 unchanged.
limma machine-learning batch-effect
updated 17 months ago by 45k • written 5.2 years ago by 22k
1
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1.5k
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Answer: A: Batch correct batch 2 while leaving batch 1 unchanged.
5.2 years ago by i.sudbery 22k
3
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1
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5.0k
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Answer: A: Small Sample Size (2 vs 3) in RNA-Seq DGE Shows Statistically Significant Result
5.2 years ago by i.sudbery 22k
1
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0
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1.4k
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Answer: A: How to perform batch correction when we have only single condition?
5.2 years ago by i.sudbery 22k
2
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2
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3.5k
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Answer: A: Adding a UMI tag to the UMI sequences in FASTQ files
5.2 years ago by i.sudbery 22k
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0
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3.5k
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Comment: C: Adding a UMI tag to the UMI sequences in FASTQ files
5.2 years ago by i.sudbery 22k
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0
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4.5k
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Comment: C: Generate gene level TPM from quant.sf file generated in salmon
5.2 years ago by i.sudbery 22k
1
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1
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190k
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Comment: C: Fold change - a final explanation
5.2 years ago by i.sudbery 22k
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0
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1.2k
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Comment: C: Split RNA Seq reads
5.2 years ago by i.sudbery 22k
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0
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2.1k
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Comment: C: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
5.2 years ago by i.sudbery 22k
2
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1
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2.1k
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Answer: A: Does BWA MEM understand paired-end suffixes? /2 in a single FASTQ file?
5.2 years ago by i.sudbery 22k
1
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0
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971
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Answer: A: Tophat / output without XS
5.2 years ago by i.sudbery 22k
0
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1
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1.7k
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Comment: C: Using of GSEA to compare RNA seq data with published gene sets?
5.2 years ago by i.sudbery 22k
0
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0
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1.7k
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Comment: C: Using of GSEA to compare RNA seq data with published gene sets?
5.2 years ago by i.sudbery 22k
1
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1
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2.9k
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Comment: C: Why does umi_tools dedup not write anything in the deduplicated.bam file?
5.3 years ago by i.sudbery 22k
0
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1
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2.9k
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Comment: C: Why does umi_tools dedup not write anything in the deduplicated.bam file?
5.3 years ago by i.sudbery 22k
0
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1
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4.3k
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Comment: C: Is there a tool to find the correct percentage of duplication levels in FastQ ?
5.3 years ago by i.sudbery 22k
1
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1
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2.9k
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Comment: C: Why does umi_tools dedup not write anything in the deduplicated.bam file?
5.3 years ago by i.sudbery 22k
1
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0
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943
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Selection of start codons in Ensembl
Ensembl Annotation Gene models
5.3 years ago by i.sudbery 22k
6
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0
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2.1k
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Answer: A: What is the importance of the rlog function (DESeq2) for downstream analysis?
5.3 years ago by i.sudbery 22k
0
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2
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2.9k
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Comment: C: How can I count the number of UMIs and reads at each position after mapping with
5.3 years ago by i.sudbery 22k
1
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2
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2.9k
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Answer: A: How can I count the number of UMIs and reads at each position after mapping with
5.3 years ago by i.sudbery 22k
0
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1
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1.6k
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Answer: A: How to cut some part of the header of reads in FASTQ file?
5.3 years ago by i.sudbery 22k
0
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1
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6.9k
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Comment: C: tool to analysis bulk RNAseq data with UMIs
5.3 years ago by i.sudbery 22k
1
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0
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1.9k
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Comment: C: Requirement of constant variance in limma-voom
5.3 years ago by i.sudbery 22k
0
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1
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1.9k
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Comment: C: Requirement of constant variance in limma-voom
5.3 years ago by i.sudbery 22k
3
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1
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1.9k
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Answer: A: Requirement of constant variance in limma-voom
5.3 years ago by i.sudbery 22k
0
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0
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3.4k
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Comment: C: Is there a way to change gene_id in a GTF file where gene_id is actually a gene_
5.3 years ago by i.sudbery 22k
0
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1
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3.4k
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Comment: C: Is there a way to change gene_id in a GTF file where gene_id is actually a gene_
5.3 years ago by i.sudbery 22k
1
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1
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3.4k
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Comment: C: Best way to change gene_id in a GTF file where gene_id is identical to gene_name
5.3 years ago by i.sudbery 22k
4
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1
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3.2k
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Answer: A: How important is normalization for RNA_Seq data ?
5.3 years ago by i.sudbery 22k
3
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1
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5.6k
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Answer: A: Input vs IgG control for RIP-seq
5.3 years ago by i.sudbery 22k
0
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0
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863
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Answer: A: Where can I get both total RNA-seq & Chip-seq data,
5.3 years ago by i.sudbery 22k
0
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0
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1.7k
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Comment: C: How can I differentiate exogenous from endogenous transcripts in RNAseq data?
5.3 years ago by i.sudbery 22k
1
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0
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2.3k
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Comment: C: Do I have batch effect?
5.3 years ago by i.sudbery 22k
0
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1
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2.3k
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Comment: C: Do I have batch effect?
5.3 years ago by i.sudbery 22k
1
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1
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1.1k
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uORF annotation in Ensembl/GENCODE
Annotation Ensembl Gencode uORF
updated 5.3 years ago by 13k • written 5.3 years ago by 22k
1
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1
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2.3k
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Comment: C: Do I have batch effect?
5.3 years ago by i.sudbery 22k
2
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1
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2.3k
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Answer: A: Do I have batch effect?
5.3 years ago by i.sudbery 22k
0
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0
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927
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Comment: C: Deposition of small sets of human fastqs
5.3 years ago by i.sudbery 22k
0
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2
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927
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Deposition of small sets of human fastqs
ethics data submission
5.3 years ago by i.sudbery 22k
1
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0
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2.3k
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Comment: C: What could be a reason for peaks called via Macs2 not appearing as real peaks in
5.3 years ago by i.sudbery 22k
0
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0
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1.7k
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Comment: C: How to detect cis and trans protein coding genes of interested lncRNAs?
5.3 years ago by i.sudbery 22k
1
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0
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1.2k
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Answer: A: Are there prediction tools that predict tageting miRNAs based on genome sequence
5.3 years ago by i.sudbery 22k
2
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1
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1.7k
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Comment: C: How to detect cis and trans protein coding genes of interested lncRNAs?
5.3 years ago by i.sudbery 22k
0
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1
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1.5k
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Comment: C: Exceptionally high peak/reads in ATACseq bam and peak files
5.3 years ago by i.sudbery 22k
0
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1
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1.7k
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Answer: A: How to detect cis and trans protein coding genes of interested lncRNAs?
5.3 years ago by i.sudbery 22k
1
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1
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4.2k
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Comment: C: Retrieving GO mappings for GOseq analysis with non-native organism
5.3 years ago by i.sudbery 22k
6
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2
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5.6k
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Answer: A: Is Stringtie a suitable tool for both gene and transcript quantification?
5.3 years ago by i.sudbery 22k
1
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0
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6.1k
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
5.4 years ago by i.sudbery 22k
1,719 results • Page 21 of 35
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