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SEURAT : loading via h5 file and applying min.cells and min.features
seurat
updated 5 months ago by 8.6k • written 5 months ago by ▴ 500
0
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0
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454
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Answer: Answer: SEURAT : loading via h5 file and applying min.cells and min.features
updated 5 months ago by 8.6k • written 5 months ago by ▴ 500
33
votes
7
replies
31k
views
8 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 9 months ago by • 0 • written 6.4 years ago by ▴ 500
3
votes
4
replies
1.4k
views
Spatial Transcriptomics : Nanostring GeoMx DSP
Spatial Transcriptomics
updated 4 months ago by ▴ 50 • written 12 months ago by ▴ 500
1
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0
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1.4k
views
Answer: Answer: Spatial Transcriptomics : Nanostring GeoMx DSP
12 months ago by ZheFrench ▴ 500
4
votes
2
replies
1.5k
views
Filter loom file using cell ids in R using seurat.disk or with loompy in python
loompy cells single seurat
updated 8 months ago by ▴ 10 • written 17 months ago by ▴ 500
3
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1
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1.5k
views
Answer: Answer: Filter loom file using cell ids in R using seurat.disk or with loompy in python
17 months ago by ZheFrench ▴ 500
0
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0
replies
908
views
Comment: Comment: Naïve question about LC-MS/MS proteomic datasets : looking for ressources, studi
17 months ago by ZheFrench ▴ 500
1
vote
2
replies
908
views
Naïve question about LC-MS/MS proteomic datasets : looking for ressources, studies with available data
proteomic
17 months ago by ZheFrench ▴ 500
1
vote
0
replies
346
views
logFoldChange computed by EdgeR different from naive log2FCcomputed based on reads
foldchange edgeR
22 months ago by ZheFrench ▴ 500
13
votes
6
replies
17k
views
Trimming TruSeq Universal Adapter (Trimmomatic)
fastq trimming RNA-Seq Trimmomatic
updated 22 months ago by • 0 • written 6.3 years ago by ▴ 500
1
vote
1
reply
1.9k
views
Filter SingleCellExperiment object just by one gene expression
SingleCellExperiment
updated 23 months ago by 3.5k • written 23 months ago by ▴ 500
1
vote
1
reply
624
views
Normalisation before edgeR for RNA-Seq
rna-seq edgeR
updated 23 months ago by 70k • written 23 months ago by ▴ 500
0
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1
reply
3.3k
views
Comment: Comment: Single Cell Experiment object to Seurat without losing rowData / colData
23 months ago by ZheFrench ▴ 500
2
votes
3
replies
3.3k
views
Single Cell Experiment object to Seurat without losing rowData / colData
scrna-seq seurat sce
updated 23 months ago by ★ 14k • written 23 months ago by ▴ 500
0
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0
replies
1.3k
views
Comment: C: Normalise batch effects for Percent Spliced In (PSI) matrice
3.0 years ago by ZheFrench ▴ 500
1
vote
2
replies
2.2k
views
DESEQ2 : plotPCA
RNA-Seq DESEQ2 PCA
updated 11 months ago by ★ 2.1k • written 3.1 years ago by ▴ 500
1
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1
reply
2.2k
views
Answer: A: DESEQ2 : plotPCA
3.1 years ago by ZheFrench ▴ 500
8
votes
1
reply
5.8k
views
R survival analysis : surv_pvalue vs fit.coxph for log-rank-test pvalue
survival analysis R
updated 3.4 years ago by 84k • written 3.4 years ago by ▴ 500
2
votes
1
reply
2.6k
views
Use PWM from CISBP-rna to find motif with MEME (FIMO)
CISBP MEME motif
updated 3.4 years ago by ▴ 580 • written 5.3 years ago by ▴ 500
4
votes
5
replies
4.3k
views
UCSC Viewer : Adjust all tracks on the same scale at the same time.
UCSC viewer visualisation
updated 3.4 years ago by ▴ 450 • written 6.3 years ago by ▴ 500
2
votes
3
replies
703
views
Advices for Single Cell analysis. Softwares to go ?
single Cells
3.7 years ago by ZheFrench ▴ 500
1
vote
0
replies
1.3k
views
Survival TCGA PAM50 : Basal vs Luminal A
survival TCGA Cancer
3.8 years ago by ZheFrench ▴ 500
3
votes
2
replies
5.7k
views
Answer: A: How to convert log2FC (Fold Change) obtained by differential expression analysis
4.0 years ago by ZheFrench ▴ 500
1
vote
2
replies
1.3k
views
Normalise batch effects for Percent Spliced In (PSI) matrice
combat sva splicing
4.2 years ago by ZheFrench ▴ 500
4
votes
2
replies
2.7k
views
Difference in duplicate number with samtools flagstat and multiqc/fastqc
fastqc multiqc duplicates chipseq samtools
updated 4.3 years ago by ★ 1.1k • written 5.8 years ago by ▴ 500
4
votes
3
replies
1.2k
views
FastQ ColorSpace to BaseSpace format in 2018
colorbase
updated 4.3 years ago by 34k • written 4.4 years ago by ▴ 500
8
votes
7
replies
1.6k
views
DESEQ2 size factors change when number of samples change in the design
DESEQ2
updated 4.4 years ago by ▴ 910 • written 4.5 years ago by ▴ 500
1
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1
reply
1.1k
views
How to visualise/explore Hi-C maps per chromosome at 100Kb and 40Kb
Hic
updated 4.4 years ago by 34k • written 4.4 years ago by ▴ 500
3
votes
3
replies
2.6k
views
BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
R genome version assembly
updated 4.4 years ago by 13k • written 4.5 years ago by ▴ 500
0
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2
replies
1.6k
views
Comment: C: DESEQ2 size factors change when number of samples change in the design
4.5 years ago by ZheFrench ▴ 500
3
votes
2
replies
5.9k
views
Heatmap with normalised count from DESEQ2
deseq2 heatmap
updated 4.5 years ago by ▴ 610 • written 4.5 years ago by ▴ 500
0
votes
3
replies
1.0k
views
How to separe eRNA by orientation from with GRO-SEQ data
GRO-SEQ eRNA
updated 4.6 years ago by • 0 • written 5.0 years ago by ▴ 500
0
votes
1
reply
1.6k
views
Comment: C: How to define Basal B subtype from TCGA breast cancer patient samples ?
4.6 years ago by ZheFrench ▴ 500
0
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3
replies
1.6k
views
How to define Basal B subtype from TCGA breast cancer patient samples ?
cancer tcga
4.6 years ago by ZheFrench ▴ 500
0
votes
2
replies
31k
views
Comment: A: ATAC-seq peak calling with MACS
4.9 years ago by ZheFrench ▴ 500
0
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1
reply
1.9k
views
Comment: C: Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
4.9 years ago by ZheFrench ▴ 500
1
vote
3
replies
1.9k
views
Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
DEEPTOOLS
updated 4.9 years ago by 103k • written 4.9 years ago by ▴ 500
5
votes
8
replies
5.1k
views
Cytoscape : how to color same nodes with several colors ?
Cytoscape
updated 5.0 years ago by ▴ 600 • written 5.0 years ago by ▴ 500
0
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0
replies
5.1k
views
Comment: C: Cytoscape : how to color same nodes with several colors ?
5.0 years ago by ZheFrench ▴ 500
0
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1
reply
5.1k
views
Comment: C: Cytoscape : how to color same nodes with several colors ?
5.0 years ago by ZheFrench ▴ 500
0
votes
0
replies
1.0k
views
Comment: C: How to separe eRNA by orientation from with GRO-SEQ data
5.0 years ago by ZheFrench ▴ 500
3
votes
2
replies
1.4k
views
TSS coordinates from Ensembl Biomart
ensembl biomart
updated 5.1 years ago by 20 • written 5.1 years ago by ▴ 500
1
vote
1
reply
2.0k
views
How to get Transcription End site (TES) via ensembl biomart ?
ensembl biomart
updated 5.1 years ago by ★ 2.2k • written 5.1 years ago by ▴ 500
7
votes
4
replies
4.8k
views
Why sequence is unmapped by bwa but position is given in Sam file and also can be aligned by blat ?
alignment sequence
updated 6 weeks ago by 38k • written 7.9 years ago by ▴ 500
0
votes
0
replies
991
views
Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
deeptools pysam HTSEQ
5.2 years ago by ZheFrench ▴ 500
0
votes
0
replies
682
views
How to get flanking intron sizes for genomic exon coordinates ?
gtf annotation
5.2 years ago by ZheFrench ▴ 500
0
votes
0
replies
7.3k
views
Comment: C: Trim galore terminates with exit signal: '256'
5.3 years ago by ZheFrench ▴ 500
0
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1
reply
7.3k
views
Comment: A: Trim galore terminates with exit signal: '256'
5.3 years ago by ZheFrench ▴ 500
1
vote
6
replies
2.2k
views
Salmon and reads order in fastq in quasi-mapping-based mode
Salmon
updated 5.3 years ago by 70k • written 5.3 years ago by ▴ 500
74 results • Page 1 of 2
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