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Comment: Comment: How to decide what gene set libraries to use in your GSEA analysis
14 months ago by e.r.zakiev ▴ 230
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Comment: Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
14 months ago by e.r.zakiev ▴ 230
17
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When should I NOT apply batch correction for my single-cell RNAseq data?
scRNA-seq batch-correction
updated 14 months ago by 44k • written 14 months ago by ▴ 230
3
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Answer: Answer: Good alignment rate for DNA-seq data
14 months ago by e.r.zakiev ▴ 230
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811
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Comment: Comment: Cloud Computing w.r.t. AWS, Google Cloud, Microsoft Azure
14 months ago by e.r.zakiev ▴ 230
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Comment: Comment: remove batch effect
14 months ago by e.r.zakiev ▴ 230
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1.6k
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Comment: Comment: Why is chromHMM's binarizeBed with the -peaks argument not recommended for broad
15 months ago by e.r.zakiev ▴ 230
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1.7k
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Comment: Comment: Extract RPKM values from Diffbind
15 months ago by e.r.zakiev ▴ 230
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1
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970
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
16 months ago by e.r.zakiev ▴ 230
0
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1
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970
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
16 months ago by e.r.zakiev ▴ 230
6
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5
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970
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barcodes not show up in overrepresented sequences in FASTQC
ribo-seq barcodes
updated 16 months ago by 148k • written 16 months ago by ▴ 230
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720
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Answer: Answer: Where can I find a TF-target gene network for skin tissue
17 months ago by e.r.zakiev ▴ 230
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579
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Comment: Comment: Panther db Reference List
18 months ago by e.r.zakiev ▴ 230
3
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2
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579
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Panther db Reference List
pantherdb enrichment-tests
updated 18 months ago by 44k • written 18 months ago by ▴ 230
3
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750
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Answer: Answer: Sewage covid sequence analysis using C-Wap
18 months ago by e.r.zakiev ▴ 230
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39k
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Comment: Comment: ATAC-seq peak calling with MACS
20 months ago by e.r.zakiev ▴ 230
3
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1
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568
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Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq ChIPseeker GO
updated 20 months ago by 44k • written 20 months ago by ▴ 230
2
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Answer: Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
20 months ago by e.r.zakiev ▴ 230
0
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3.7k
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Comment: Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
20 months ago by e.r.zakiev ▴ 230
0
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1
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1.6k
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Comment: Comment: msigdbr returns the same genesets for mouse as in for human,
20 months ago by e.r.zakiev ▴ 230
1
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2.3k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
21 months ago by e.r.zakiev ▴ 230
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
21 months ago by e.r.zakiev ▴ 230
0
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1.6k
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Comment: Comment: msigdbr returns the same genesets for mouse as in for human,
21 months ago by e.r.zakiev ▴ 230
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6.1k
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Comment: Comment: Ensembl Hg38 dna, dna_rm, and dna_sm
21 months ago by e.r.zakiev ▴ 230
2
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5
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1.6k
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msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 20 months ago by 13k • written 21 months ago by ▴ 230
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0
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20k
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Comment: Comment: Cell Type Marker Databases?
21 months ago by e.r.zakiev ▴ 230
12
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8
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2.3k
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Sorting a STAR-output bam file with samtools leads to a significant reduction in size of the sorted bam file
samtools STAR
21 months ago by e.r.zakiev ▴ 230
0
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0
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11k
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Comment: Comment: How to submit multithreaded jobs on SLURM and determine number of threads?
21 months ago by e.r.zakiev ▴ 230
0
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524
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Double-pass with STAR for better detection of spliced variants in assessing quality of FFPE RNAseq data: should I go for it?
RNA-seq STAR
updated 21 months ago by 44k • written 21 months ago by ▴ 230
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3.0k
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Comment: Comment: Splice aware vs splice unaware aligners?
21 months ago by e.r.zakiev ▴ 230
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46k
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Comment: Comment: Snakemake vs. Nextflow: strengths and weaknesses
21 months ago by e.r.zakiev ▴ 230
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38k
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Comment: Comment: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
21 months ago by e.r.zakiev ▴ 230
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1
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5.1k
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Comment: Comment: What does the decimal ending of a transcript id mean?
21 months ago by e.r.zakiev ▴ 230
3
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1
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836
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Which reference transcriptome/genome to use for mus musculus if I know the particular strain involved in the experiment?
mice alignment genome transcriptome
updated 21 months ago by 44k • written 21 months ago by ▴ 230
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20k
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Comment: Comment: RNA-Seq analysis using STAR and Salmon
21 months ago by e.r.zakiev ▴ 230
0
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1
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1.8k
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Comment: Comment: Reference genome
21 months ago by e.r.zakiev ▴ 230
0
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0
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1.8k
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Comment: Comment: blast engine error empty blast query vector
21 months ago by e.r.zakiev ▴ 230
4
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1
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669
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TruSeq Illumina adapters are BLASTed with a high confidence to some genes/terms
RNAseq adapters Truseq BLAST
updated 22 months ago by 85k • written 22 months ago by ▴ 230
0
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5.4k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
2.1 years ago by e.r.zakiev ▴ 230
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0
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5.4k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
2.1 years ago by e.r.zakiev ▴ 230
1
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967
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Answer: Answer: Gene Rank for GSEA Preranked analysis?
2.1 years ago by e.r.zakiev ▴ 230
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