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2
votes
1
reply
330
views
Looking for ressource/database of gene expression matrix for PDX mapped over human AND mouse
database PDX
4 months ago by ZheFrench ▴ 590
2
votes
0
replies
330
views
Answer: Answer: Looking for ressource/database of gene expression matrix for PDX mapped over hum
4 months ago by ZheFrench ▴ 590
1
vote
1
reply
1.0k
views
logFoldChange computed by EdgeR different from naive log2FCcomputed based on reads
edgeR fold-change
updated 12 months ago by ★ 7.8k • written 3.8 years ago by ▴ 590
0
votes
1
reply
473
views
double @HD header for bam
bam
updated 14 months ago by 44k • written 14 months ago by ▴ 590
0
votes
1
reply
2.7k
views
SEURAT : loading via h5 file and applying min.cells and min.features
seurat
updated 2.4 years ago by 9.0k • written 2.4 years ago by ▴ 590
0
votes
0
replies
2.7k
views
Answer: Answer: SEURAT : loading via h5 file and applying min.cells and min.features
updated 2.4 years ago by 9.0k • written 2.4 years ago by ▴ 590
53
votes
9
replies
53k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 12 months ago by ▴ 650 • written 8.3 years ago by ▴ 590
3
votes
4
replies
3.8k
views
Spatial Transcriptomics : Nanostring GeoMx DSP
Spatial Transcriptomics
updated 2.3 years ago by ▴ 50 • written 2.9 years ago by ▴ 590
1
vote
0
replies
3.8k
views
Answer: Answer: Spatial Transcriptomics : Nanostring GeoMx DSP
2.9 years ago by ZheFrench ▴ 590
6
votes
2
replies
3.2k
views
Filter loom file using cell ids in R using seurat.disk or with loompy in python
loompy cells single seurat
updated 2.6 years ago by ▴ 10 • written 3.4 years ago by ▴ 590
3
votes
1
reply
3.2k
views
Answer: Answer: Filter loom file using cell ids in R using seurat.disk or with loompy in python
3.4 years ago by ZheFrench ▴ 590
0
votes
0
replies
1.3k
views
Comment: Comment: Naïve question about LC-MS/MS proteomic datasets : looking for ressources, studi
3.4 years ago by ZheFrench ▴ 590
1
vote
2
replies
1.3k
views
Naïve question about LC-MS/MS proteomic datasets : looking for ressources, studies with available data
proteomic
3.4 years ago by ZheFrench ▴ 590
13
votes
6
replies
21k
views
Trimming TruSeq Universal Adapter (Trimmomatic)
fastq trimming RNA-Seq Trimmomatic
updated 3.8 years ago by • 0 • written 8.2 years ago by ▴ 590
1
vote
1
reply
3.6k
views
Filter SingleCellExperiment object just by one gene expression
SingleCellExperiment
updated 3.8 years ago by 4.1k • written 3.8 years ago by ▴ 590
1
vote
1
reply
1.0k
views
Normalisation before edgeR for RNA-Seq
rna-seq edgeR
updated 3.8 years ago by 86k • written 3.8 years ago by ▴ 590
0
votes
1
reply
7.9k
views
Comment: Comment: Single Cell Experiment object to Seurat without losing rowData / colData
3.9 years ago by ZheFrench ▴ 590
3
votes
3
replies
7.9k
views
Single Cell Experiment object to Seurat without losing rowData / colData
scrna-seq seurat sce
updated 3.9 years ago by ★ 18k • written 3.9 years ago by ▴ 590
0
votes
0
replies
2.0k
views
Comment: C: Normalise batch effects for Percent Spliced In (PSI) matrice
4.9 years ago by ZheFrench ▴ 590
1
vote
1
reply
3.1k
views
Answer: A: DESEQ2 : plotPCA
5.0 years ago by ZheFrench ▴ 590
1
vote
2
replies
3.1k
views
DESEQ2 : plotPCA
RNA-Seq DESEQ2 PCA
updated 2.8 years ago by ★ 2.2k • written 5.0 years ago by ▴ 590
8
votes
1
reply
7.7k
views
R survival analysis : surv_pvalue vs fit.coxph for log-rank-test pvalue
survival analysis R
updated 5.3 years ago by 89k • written 5.3 years ago by ▴ 590
2
votes
1
reply
3.4k
views
Use PWM from CISBP-rna to find motif with MEME (FIMO)
CISBP MEME motif
updated 5.3 years ago by ★ 1.3k • written 7.2 years ago by ▴ 590
4
votes
5
replies
5.5k
views
UCSC Viewer : Adjust all tracks on the same scale at the same time.
UCSC viewer visualisation
updated 5.4 years ago by ▴ 480 • written 8.3 years ago by ▴ 590
2
votes
3
replies
1.0k
views
Advices for Single Cell analysis. Softwares to go ?
single Cells
5.6 years ago by ZheFrench ▴ 590
1
vote
0
replies
1.7k
views
Survival TCGA PAM50 : Basal vs Luminal A
survival TCGA Cancer
5.7 years ago by ZheFrench ▴ 590
3
votes
2
replies
7.0k
views
Answer: A: How to convert log2FC (Fold Change) obtained by differential expression analysis
5.9 years ago by ZheFrench ▴ 590
1
vote
3
replies
2.0k
views
Normalise batch effects for Percent Spliced In (PSI) matrice
combat sva splicing
updated 11 months ago by ▴ 70 • written 6.1 years ago by ▴ 590
4
votes
2
replies
3.4k
views
Difference in duplicate number with samtools flagstat and multiqc/fastqc
fastqc multiqc duplicates chipseq samtools
updated 6.2 years ago by ★ 1.4k • written 7.7 years ago by ▴ 590
4
votes
3
replies
1.6k
views
FastQ ColorSpace to BaseSpace format in 2018
colorbase
updated 6.3 years ago by 35k • written 6.3 years ago by ▴ 590
8
votes
7
replies
2.5k
views
DESEQ2 size factors change when number of samples change in the design
DESEQ2
updated 6.3 years ago by ▴ 960 • written 6.4 years ago by ▴ 590
1
vote
1
reply
1.5k
views
How to visualise/explore Hi-C maps per chromosome at 100Kb and 40Kb
Hic
updated 6.3 years ago by 36k • written 6.3 years ago by ▴ 590
3
votes
3
replies
3.6k
views
BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
R genome version assembly
updated 6.3 years ago by 13k • written 6.4 years ago by ▴ 590
0
votes
2
replies
2.5k
views
Comment: C: DESEQ2 size factors change when number of samples change in the design
6.4 years ago by ZheFrench ▴ 590
3
votes
2
replies
7.4k
views
Heatmap with normalised count from DESEQ2
deseq2 heatmap
updated 6.4 years ago by ▴ 640 • written 6.4 years ago by ▴ 590
0
votes
3
replies
1.4k
views
How to separe eRNA by orientation from with GRO-SEQ data
GRO-SEQ eRNA
updated 6.5 years ago by • 0 • written 6.9 years ago by ▴ 590
0
votes
1
reply
2.0k
views
Comment: C: How to define Basal B subtype from TCGA breast cancer patient samples ?
6.5 years ago by ZheFrench ▴ 590
0
votes
3
replies
2.0k
views
How to define Basal B subtype from TCGA breast cancer patient samples ?
cancer tcga
6.5 years ago by ZheFrench ▴ 590
0
votes
2
replies
39k
views
Comment: A: ATAC-seq peak calling with MACS
6.8 years ago by ZheFrench ▴ 590
0
votes
1
reply
2.5k
views
Comment: C: Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
6.8 years ago by ZheFrench ▴ 590
1
vote
3
replies
2.5k
views
Can't upgrade deeptools 2.5.7 to 3.0 via conda 4.5.0 on Debian Jessie
DEEPTOOLS
updated 6.9 years ago by 105k • written 6.9 years ago by ▴ 590
5
votes
8
replies
6.1k
views
Cytoscape : how to color same nodes with several colors ?
Cytoscape
updated 6.9 years ago by ▴ 620 • written 6.9 years ago by ▴ 590
0
votes
0
replies
6.1k
views
Comment: C: Cytoscape : how to color same nodes with several colors ?
6.9 years ago by ZheFrench ▴ 590
0
votes
1
reply
6.1k
views
Comment: C: Cytoscape : how to color same nodes with several colors ?
6.9 years ago by ZheFrench ▴ 590
0
votes
0
replies
1.4k
views
Comment: C: How to separe eRNA by orientation from with GRO-SEQ data
6.9 years ago by ZheFrench ▴ 590
3
votes
2
replies
1.8k
views
TSS coordinates from Ensembl Biomart
ensembl biomart
updated 7.0 years ago by 20 • written 7.1 years ago by ▴ 590
1
vote
1
reply
2.6k
views
How to get Transcription End site (TES) via ensembl biomart ?
ensembl biomart
updated 7.0 years ago by ★ 2.4k • written 7.0 years ago by ▴ 590
7
votes
4
replies
5.7k
views
Why sequence is unmapped by bwa but position is given in Sam file and also can be aligned by blat ?
alignment sequence
updated 2.0 years ago by 44k • written 9.8 years ago by ▴ 590
0
votes
0
replies
1.2k
views
Estimate Fragment Size from Single End ChipSeq with (pysam, htseq lib or deeptools API)
deeptools pysam HTSEQ
7.1 years ago by ZheFrench ▴ 590
0
votes
0
replies
902
views
How to get flanking intron sizes for genomic exon coordinates ?
gtf annotation
7.1 years ago by ZheFrench ▴ 590
77 results • Page 1 of 2
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