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Comment: Comment: Clustering in single cell
2.1 years ago by e.r.zakiev ▴ 260
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Comment: Comment: Clustering resolution single-cell RNA-seq
2.1 years ago by e.r.zakiev ▴ 260
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6.9k
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Comment: Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
2.1 years ago by e.r.zakiev ▴ 260
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Comment: Comment: Good alignment rate for DNA-seq data
2.1 years ago by e.r.zakiev ▴ 260
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6.9k
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Comment: Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
2.1 years ago by e.r.zakiev ▴ 260
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0
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6.9k
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Comment: Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
2.1 years ago by e.r.zakiev ▴ 260
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3.4k
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Answer: Answer: How to decide what gene set libraries to use in your GSEA analysis
2.1 years ago by e.r.zakiev ▴ 260
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0
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3.4k
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Comment: Comment: How to decide what gene set libraries to use in your GSEA analysis
2.1 years ago by e.r.zakiev ▴ 260
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6.9k
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Comment: Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
2.1 years ago by e.r.zakiev ▴ 260
18
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7
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6.9k
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When should I NOT apply batch correction for my single-cell RNAseq data?
scRNA-seq batch-correction
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 260
3
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2
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3.1k
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Answer: Answer: Good alignment rate for DNA-seq data
2.1 years ago by e.r.zakiev ▴ 260
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1.3k
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Comment: Comment: Cloud Computing w.r.t. AWS, Google Cloud, Microsoft Azure
2.1 years ago by e.r.zakiev ▴ 260
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2.8k
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Comment: Comment: remove batch effect
2.1 years ago by e.r.zakiev ▴ 260
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2.0k
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Comment: Comment: Why is chromHMM's binarizeBed with the -peaks argument not recommended for broad
2.2 years ago by e.r.zakiev ▴ 260
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2.3k
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Comment: Comment: Extract RPKM values from Diffbind
2.2 years ago by e.r.zakiev ▴ 260
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1.5k
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
2.3 years ago by e.r.zakiev ▴ 260
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1
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1.5k
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
2.3 years ago by e.r.zakiev ▴ 260
6
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5
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1.5k
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barcodes not show up in overrepresented sequences in FASTQC
ribo-seq barcodes
updated 2.3 years ago by 154k • written 2.3 years ago by ▴ 260
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996
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Answer: Answer: Where can I find a TF-target gene network for skin tissue
2.4 years ago by e.r.zakiev ▴ 260
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920
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Comment: Comment: Panther db Reference List
2.4 years ago by e.r.zakiev ▴ 260
3
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2
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920
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Panther db Reference List
pantherdb enrichment-tests
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 260
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1.1k
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Answer: Answer: Sewage covid sequence analysis using C-Wap
2.5 years ago by e.r.zakiev ▴ 260
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43k
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Comment: Comment: ATAC-seq peak calling with MACS
2.6 years ago by e.r.zakiev ▴ 260
3
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1
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890
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Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq ChIPseeker GO
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 260
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Answer: Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
2.6 years ago by e.r.zakiev ▴ 260
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1
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5.8k
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Comment: Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
2.6 years ago by e.r.zakiev ▴ 260
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1
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2.5k
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Comment: Comment: msigdbr returns the same genesets for mouse as in for human,
2.6 years ago by e.r.zakiev ▴ 260
1
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0
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4.0k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
2.6 years ago by e.r.zakiev ▴ 260
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4.0k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
2.6 years ago by e.r.zakiev ▴ 260
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0
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2.5k
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Comment: Comment: msigdbr returns the same genesets for mouse as in for human,
2.6 years ago by e.r.zakiev ▴ 260
0
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0
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7.3k
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Comment: Comment: Ensembl Hg38 dna, dna_rm, and dna_sm
2.6 years ago by e.r.zakiev ▴ 260
2
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5
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2.5k
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msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 2.6 years ago by 13k • written 2.6 years ago by ▴ 260
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23k
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Comment: Comment: Cell Type Marker Databases?
2.6 years ago by e.r.zakiev ▴ 260
12
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8
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4.0k
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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
2.6 years ago by e.r.zakiev ▴ 260
0
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0
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13k
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Comment: Comment: How to submit multithreaded jobs on SLURM and determine number of threads?
2.7 years ago by e.r.zakiev ▴ 260
0
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0
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690
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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 2.7 years ago by 45k • written 2.7 years ago by ▴ 260
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4.0k
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Comment: Comment: Splice aware vs splice unaware aligners?
2.7 years ago by e.r.zakiev ▴ 260
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51k
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Comment: Comment: Snakemake vs. Nextflow: strengths and weaknesses
2.7 years ago by e.r.zakiev ▴ 260
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42k
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Comment: Comment: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
2.7 years ago by e.r.zakiev ▴ 260
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5.9k
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Comment: Comment: What does the decimal ending of a transcript id mean?
2.7 years ago by e.r.zakiev ▴ 260
3
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1
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1.2k
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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 2.7 years ago by 45k • written 2.7 years ago by ▴ 260
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24k
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Comment: Comment: RNA-Seq analysis using STAR and Salmon
2.7 years ago by e.r.zakiev ▴ 260
0
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1
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2.7k
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Comment: Comment: Reference genome
2.7 years ago by e.r.zakiev ▴ 260
0
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2.5k
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Comment: Comment: blast engine error empty blast query vector
2.7 years ago by e.r.zakiev ▴ 260
4
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1
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994
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TruSeq Illumina adapters are BLASTed with a high confidence to some genes/terms
RNAseq adapters Truseq BLAST
updated 2.7 years ago by 90k • written 2.7 years ago by ▴ 260
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7.4k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
3.0 years ago by e.r.zakiev ▴ 260
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0
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7.4k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
3.0 years ago by e.r.zakiev ▴ 260
1
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0
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1.4k
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Answer: Answer: Gene Rank for GSEA Preranked analysis?
3.0 years ago by e.r.zakiev ▴ 260
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