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729
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logFoldChange computed by EdgeR different from naive log2FCcomputed based on reads
edgeR fold-change
updated 11 weeks ago by ★ 7.0k • written 2.9 years ago by ▴ 570
0
votes
1
reply
320
views
double @HD header for bam
bam
updated 4 months ago by 43k • written 4 months ago by ▴ 570
0
votes
1
reply
2.0k
views
SEURAT : loading via h5 file and applying min.cells and min.features
seurat
updated 19 months ago by 8.9k • written 19 months ago by ▴ 570
0
votes
0
replies
2.0k
views
Answer: Answer: SEURAT : loading via h5 file and applying min.cells and min.features
updated 19 months ago by 8.9k • written 19 months ago by ▴ 570
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 12 weeks ago by ▴ 640 • written 7.5 years ago by ▴ 570
3
votes
4
replies
2.9k
views
Spatial Transcriptomics : Nanostring GeoMx DSP
Spatial Transcriptomics
updated 18 months ago by ▴ 50 • written 2.1 years ago by ▴ 570
1
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0
replies
2.9k
views
Answer: Answer: Spatial Transcriptomics : Nanostring GeoMx DSP
2.1 years ago by ZheFrench ▴ 570
6
votes
2
replies
2.6k
views
Filter loom file using cell ids in R using seurat.disk or with loompy in python
loompy cells single seurat
updated 21 months ago by ▴ 10 • written 2.5 years ago by ▴ 570
3
votes
1
reply
2.6k
views
Answer: Answer: Filter loom file using cell ids in R using seurat.disk or with loompy in python
2.5 years ago by ZheFrench ▴ 570
0
votes
0
replies
1.1k
views
Comment: Comment: Naïve question about LC-MS/MS proteomic datasets : looking for ressources, studi
2.6 years ago by ZheFrench ▴ 570
1
vote
2
replies
1.1k
views
Naïve question about LC-MS/MS proteomic datasets : looking for ressources, studies with available data
proteomic
2.6 years ago by ZheFrench ▴ 570
13
votes
6
replies
19k
views
Trimming TruSeq Universal Adapter (Trimmomatic)
fastq trimming RNA-Seq Trimmomatic
updated 3.0 years ago by • 0 • written 7.4 years ago by ▴ 570
1
vote
1
reply
3.0k
views
Filter SingleCellExperiment object just by one gene expression
SingleCellExperiment
updated 3.0 years ago by 3.9k • written 3.0 years ago by ▴ 570
1
vote
1
reply
817
views
Normalisation before edgeR for RNA-Seq
rna-seq edgeR
updated 3.0 years ago by 81k • written 3.0 years ago by ▴ 570
0
votes
1
reply
6.3k
views
Comment: Comment: Single Cell Experiment object to Seurat without losing rowData / colData
3.0 years ago by ZheFrench ▴ 570
3
votes
3
replies
6.3k
views
Single Cell Experiment object to Seurat without losing rowData / colData
scrna-seq seurat sce
updated 3.0 years ago by ★ 16k • written 3.0 years ago by ▴ 570
0
votes
0
replies
1.7k
views
Comment: C: Normalise batch effects for Percent Spliced In (PSI) matrice
4.1 years ago by ZheFrench ▴ 570
1
vote
2
replies
2.8k
views
DESEQ2 : plotPCA
RNA-Seq DESEQ2 PCA
updated 2.0 years ago by ★ 2.2k • written 4.2 years ago by ▴ 570
1
vote
1
reply
2.8k
views
Answer: A: DESEQ2 : plotPCA
4.2 years ago by ZheFrench ▴ 570
8
votes
1
reply
7.0k
views
R survival analysis : surv_pvalue vs fit.coxph for log-rank-test pvalue
survival analysis R
updated 4.5 years ago by 87k • written 4.5 years ago by ▴ 570
2
votes
1
reply
3.0k
views
Use PWM from CISBP-rna to find motif with MEME (FIMO)
CISBP MEME motif
updated 4.5 years ago by ★ 1.1k • written 6.4 years ago by ▴ 570
4
votes
5
replies
5.0k
views
UCSC Viewer : Adjust all tracks on the same scale at the same time.
UCSC viewer visualisation
updated 4.5 years ago by ▴ 470 • written 7.4 years ago by ▴ 570
2
votes
3
replies
907
views
Advices for Single Cell analysis. Softwares to go ?
single Cells
4.8 years ago by ZheFrench ▴ 570
1
vote
0
replies
1.5k
views
Survival TCGA PAM50 : Basal vs Luminal A
survival TCGA Cancer
4.9 years ago by ZheFrench ▴ 570
3
votes
2
replies
6.5k
views
Answer: A: How to convert log2FC (Fold Change) obtained by differential expression analysis
5.1 years ago by ZheFrench ▴ 570
1
vote
3
replies
1.7k
views
Normalise batch effects for Percent Spliced In (PSI) matrice
combat sva splicing
updated 7 weeks ago by ▴ 70 • written 5.3 years ago by ▴ 570
4
votes
2
replies
3.1k
views
Difference in duplicate number with samtools flagstat and multiqc/fastqc
fastqc multiqc duplicates chipseq samtools
updated 5.4 years ago by ★ 1.4k • written 6.9 years ago by ▴ 570
4
votes
3
replies
1.4k
views
FastQ ColorSpace to BaseSpace format in 2018
colorbase
updated 5.4 years ago by 35k • written 5.5 years ago by ▴ 570
8
votes
7
replies
2.1k
views
DESEQ2 size factors change when number of samples change in the design
DESEQ2
updated 5.4 years ago by ▴ 930 • written 5.6 years ago by ▴ 570
1
vote
1
reply
1.3k
views
How to visualise/explore Hi-C maps per chromosome at 100Kb and 40Kb
Hic
updated 5.5 years ago by 35k • written 5.5 years ago by ▴ 570
3
votes
3
replies
3.2k
views
BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
R genome version assembly
updated 5.5 years ago by 13k • written 5.6 years ago by ▴ 570
0
votes
2
replies
2.1k
views
Comment: C: DESEQ2 size factors change when number of samples change in the design
5.6 years ago by ZheFrench ▴ 570
3
votes
2
replies
6.9k
views
Heatmap with normalised count from DESEQ2
deseq2 heatmap
updated 5.6 years ago by ▴ 620 • written 5.6 years ago by ▴ 570
0
votes
3
replies
1.2k
views
How to separe eRNA by orientation from with GRO-SEQ data
GRO-SEQ eRNA
updated 5.6 years ago by • 0 • written 6.1 years ago by ▴ 570
0
votes
1
reply
1.8k
views
Comment: C: How to define Basal B subtype from TCGA breast cancer patient samples ?
5.7 years ago by ZheFrench ▴ 570
0
votes
3
replies
1.8k
views
How to define Basal B subtype from TCGA breast cancer patient samples ?
cancer tcga
5.7 years ago by ZheFrench ▴ 570
0
votes
2
replies
36k
views
Comment: A: ATAC-seq peak calling with MACS
6.0 years ago by ZheFrench ▴ 570
0
votes
1
reply
2.2k
views
Comment: C: Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
6.0 years ago by ZheFrench ▴ 570
1
vote
3
replies
2.2k
views
Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
DEEPTOOLS
updated 6.0 years ago by 104k • written 6.0 years ago by ▴ 570
5
votes
8
replies
5.7k
views
Cytoscape : how to color same nodes with several colors ?
Cytoscape
updated 6.1 years ago by ▴ 620 • written 6.1 years ago by ▴ 570
0
votes
0
replies
5.7k
views
Comment: C: Cytoscape : how to color same nodes with several colors ?
6.1 years ago by ZheFrench ▴ 570
0
votes
1
reply
5.7k
views
Comment: C: Cytoscape : how to color same nodes with several colors ?
6.1 years ago by ZheFrench ▴ 570
0
votes
0
replies
1.2k
views
Comment: C: How to separe eRNA by orientation from with GRO-SEQ data
6.1 years ago by ZheFrench ▴ 570
3
votes
2
replies
1.7k
views
TSS coordinates from Ensembl Biomart
ensembl biomart
updated 6.2 years ago by 20 • written 6.2 years ago by ▴ 570
1
vote
1
reply
2.4k
views
How to get Transcription End site (TES) via ensembl biomart ?
ensembl biomart
updated 6.2 years ago by ★ 2.4k • written 6.2 years ago by ▴ 570
7
votes
4
replies
5.4k
views
Why sequence is unmapped by bwa but position is given in Sam file and also can be aligned by blat ?
alignment sequence
updated 14 months ago by 43k • written 9.0 years ago by ▴ 570
0
votes
0
replies
1.1k
views
Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
deeptools pysam HTSEQ
6.2 years ago by ZheFrench ▴ 570
0
votes
0
replies
807
views
How to get flanking intron sizes for genomic exon coordinates ?
gtf annotation
6.3 years ago by ZheFrench ▴ 570
0
votes
0
replies
8.8k
views
Comment: C: Trim galore terminates with exit signal: '256'
6.4 years ago by ZheFrench ▴ 570
0
votes
1
reply
8.8k
views
Comment: A: Trim galore terminates with exit signal: '256'
6.4 years ago by ZheFrench ▴ 570
75 results • Page 1 of 2
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