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Comment: Comment: How to decide what gene set libraries to use in your GSEA analysis
12 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?
12 months ago by e.r.zakiev ▴ 230
17
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7
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When should I NOT apply batch correction for my single-cell RNAseq data?
scRNA-seq batch-correction
updated 12 months ago by 44k • written 12 months ago by ▴ 230
3
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1.5k
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Answer: Answer: Good alignment rate for DNA-seq data
12 months ago by e.r.zakiev ▴ 230
0
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1
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762
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Comment: Comment: Cloud Computing w.r.t. AWS, Google Cloud, Microsoft Azure
12 months ago by e.r.zakiev ▴ 230
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Comment: Comment: remove batch effect
12 months ago by e.r.zakiev ▴ 230
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1.5k
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Comment: Comment: Why is chromHMM's binarizeBed with the -peaks argument not recommended for broad
13 months ago by e.r.zakiev ▴ 230
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1.6k
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Comment: Comment: Extract RPKM values from Diffbind
13 months ago by e.r.zakiev ▴ 230
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1
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915
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
15 months ago by e.r.zakiev ▴ 230
0
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1
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915
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
15 months ago by e.r.zakiev ▴ 230
6
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5
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915
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barcodes not show up in overrepresented sequences in FASTQC
ribo-seq barcodes
updated 15 months ago by 146k • written 15 months ago by ▴ 230
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705
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Answer: Answer: Where can I find a TF-target gene network for skin tissue
16 months ago by e.r.zakiev ▴ 230
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565
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Comment: Comment: Panther db Reference List
16 months ago by e.r.zakiev ▴ 230
3
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2
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565
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Panther db Reference List
pantherdb enrichment-tests
updated 16 months ago by 44k • written 16 months ago by ▴ 230
3
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721
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Answer: Answer: Sewage covid sequence analysis using C-Wap
17 months ago by e.r.zakiev ▴ 230
0
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38k
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Comment: Comment: ATAC-seq peak calling with MACS
18 months ago by e.r.zakiev ▴ 230
3
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1
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547
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Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq ChIPseeker GO
updated 18 months ago by 44k • written 18 months ago by ▴ 230
2
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3.5k
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Answer: Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
18 months ago by e.r.zakiev ▴ 230
0
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1
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3.5k
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Comment: Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
18 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,
19 months ago by e.r.zakiev ▴ 230
1
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2.1k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
19 months ago by e.r.zakiev ▴ 230
0
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2.1k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
19 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,
19 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
19 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 19 months ago by 13k • written 19 months ago by ▴ 230
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0
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20k
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Comment: Comment: Cell Type Marker Databases?
19 months ago by e.r.zakiev ▴ 230
12
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8
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2.1k
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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
19 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?
19 months ago by e.r.zakiev ▴ 230
0
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506
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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 19 months ago by 44k • written 19 months ago by ▴ 230
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2.8k
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Comment: Comment: Splice aware vs splice unaware aligners?
19 months ago by e.r.zakiev ▴ 230
0
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0
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45k
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Comment: Comment: Snakemake vs. Nextflow: strengths and weaknesses
19 months ago by e.r.zakiev ▴ 230
0
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37k
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Comment: Comment: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
19 months ago by e.r.zakiev ▴ 230
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1
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5.0k
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Comment: Comment: What does the decimal ending of a transcript id mean?
19 months ago by e.r.zakiev ▴ 230
3
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1
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807
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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 19 months ago by 44k • written 19 months ago by ▴ 230
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19k
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Comment: Comment: RNA-Seq analysis using STAR and Salmon
19 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
19 months ago by e.r.zakiev ▴ 230
0
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0
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1.7k
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Comment: Comment: blast engine error empty blast query vector
19 months ago by e.r.zakiev ▴ 230
4
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1
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651
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TruSeq Illumina adapters are BLASTed with a high confidence to some genes/terms
RNAseq adapters Truseq BLAST
updated 20 months ago by 85k • written 20 months ago by ▴ 230
0
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0
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5.3k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
24 months ago by e.r.zakiev ▴ 230
0
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0
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5.3k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
24 months ago by e.r.zakiev ▴ 230
1
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0
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921
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Answer: Answer: Gene Rank for GSEA Preranked analysis?
24 months ago by e.r.zakiev ▴ 230
91 results • Page 2 of 2
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