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questions
2
votes
2
replies
178
views
statistical testing for MS/MS proteomics bulk samples
DEG
proteomics
updated 5 days ago by
ATpoint
85k • written 5 days ago by
QX
▴ 60
2
votes
4
replies
315
views
coordinate vs contributions for the variables in PCA using FactoMineR
PCA
updated 10 days ago by
Bastien Hervé
5.8k • written 10 days ago by
QX
▴ 60
3
votes
6
replies
443
views
PCA for count data
PCA
18 days ago by
QX
▴ 60
0
votes
3
replies
454
views
DEseq2 with different designs matrix
DEseq2
8 weeks ago by
QX
▴ 60
0
votes
0
replies
146
views
Different position for same gene using annotatePeak from ChIPseeker
ChIPseeker
ATACseq
9 weeks ago by
QX
▴ 60
0
votes
0
replies
149
views
plotHeatmap from deeptools explain
atac-seq
9 weeks ago by
QX
▴ 60
5
votes
4
replies
530
views
difference between macs2 callpeak using bam and bed file
macs2
atac-seq
10 weeks ago by
QX
▴ 60
2
votes
5
replies
460
views
call peak for all replicates in all conditions using macs2
macs2
ATACseq
updated 11 weeks ago by
zau saa
▴ 150 • written 11 weeks ago by
QX
▴ 60
1
vote
4
replies
387
views
trimming 151bp to shorter k-mer in ATAC-seq analysis
ATAC-seq
11 weeks ago by
QX
▴ 60
3
votes
6
replies
602
views
which bed file should be used for deeptools computeMatrix
atac-seq
deeptools
updated 12 weeks ago by
Ming Tommy Tang
★ 4.5k • written 12 weeks ago by
QX
▴ 60
0
votes
0
replies
179
views
reference-point setting from computeMatrix
ATACseq
12 weeks ago by
QX
▴ 60
0
votes
0
replies
146
views
which distance used for kmeans in deeptools plotHeatmap
atac
deeptools
12 weeks ago by
QX
▴ 60
1
vote
1
reply
247
views
merge replicate for bigWig files from macs2 peak calling
ATAC-seq
updated 12 weeks ago by
ATpoint
85k • written 12 weeks ago by
QX
▴ 60
4
votes
4
replies
352
views
MACS2 for multiple conditions in ATACseq analysis
mac2
3 months ago by
QX
▴ 60
4
votes
4
replies
558
views
Increase the memory and core usage of R
R
updated 3 months ago by
Mensur Dlakic
★ 28k • written 3 months ago by
QX
▴ 60
3
votes
2
replies
415
views
is that statistical correct to use DEseq2 for proteomics data
proteomics
DEseq2
updated 3 months ago by
ATpoint
85k • written 3 months ago by
QX
▴ 60
4
votes
8
replies
559
views
featureCounts output
macs2
featureCounts
updated 3 months ago by
rfran010
★ 1.3k • written 3 months ago by
QX
▴ 60
2
votes
6
replies
499
views
input for gatk VariantAnnotator --dbsnp
VariantAnnotator
gatk
updated 3 months ago by
GenoMax
146k • written 3 months ago by
QX
▴ 60
5
votes
5
replies
503
views
best way to submit hpc job using snakemake
snakemake
3 months ago by
QX
▴ 60
1
vote
3
replies
331
views
snakemake config file with path
snakemake
updated 3 months ago by
pbioinf
▴ 140 • written 3 months ago by
QX
▴ 60
0
votes
2
replies
321
views
how to colorize snakemake editing text
snakemake
updated 4 months ago by
Michael
55k • written 4 months ago by
QX
▴ 60
3
votes
5
replies
632
views
Calling variants/SNP for single-cell RNA-seq data
SNP
scRNAseq
updated 9 weeks ago by
yura.grabovska
▴ 600 • written 4 months ago by
QX
▴ 60
2
votes
1
reply
313
views
Split the fastqc file base on barcode
fastq
updated 4 months ago by
GenoMax
146k • written 4 months ago by
QX
▴ 60
2
votes
3
replies
433
views
bash for merging bam files by samtools
samtools
updated 4 months ago by
GenoMax
146k • written 4 months ago by
QX
▴ 60
5
votes
3
replies
561
views
chIP-seq vs ATACseq analysis
ATACseq
4 months ago by
QX
▴ 60
0
votes
1
reply
420
views
invalid class “Assay” object issue from Seurat
seurat
updated 4 months ago by
bk11
★ 3.0k • written 4 months ago by
QX
▴ 60
8
votes
3
replies
511
views
conda-like env for R
R
conda
updated 4 months ago by
dthorbur
★ 2.5k • written 4 months ago by
QX
▴ 60
2
votes
1
reply
296
views
Trimming from 151bp to 65bp
sequencing
data
updated 5 months ago by
GenoMax
146k • written 5 months ago by
QX
▴ 60
5
votes
11
replies
704
views
6 follow
Asking for parallel jobs setting on HPC when analyzing sequencing data
HPC
parallel
updated 5 months ago by
Darked89
4.7k • written 5 months ago by
QX
▴ 60
4
votes
2
replies
453
views
cannot conda install macs3 on linux
atac
macs3
5 months ago by
QX
▴ 60
3
votes
5
replies
686
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 5 months ago by
Pierre Lindenbaum
164k • written 5 months ago by
QX
▴ 60
3
votes
3
replies
480
views
Unexpected read length from NGS
NGS
Illumina
5 months ago by
QX
▴ 60
3
votes
4
replies
651
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
6 months ago by
QX
▴ 60
0
votes
0
replies
193
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
6 months ago by
QX
▴ 60
0
votes
0
replies
174
views
NicheNet cell-cell communication analysis outcome
nichenet
scRNA-seq
7 months ago by
QX
▴ 60
2
votes
3
replies
606
views
Annotate genes from gtf file to vcf file
gtf
genomics
vcf
7 months ago by
QX
▴ 60
0
votes
1
reply
310
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 7 months ago by
ATpoint
85k • written 7 months ago by
QX
▴ 60
0
votes
1
reply
289
views
SNP and Genes position matching dataframes in R
R
dataframe
updated 7 months ago by
dthorbur
★ 2.5k • written 7 months ago by
QX
▴ 60
2
votes
1
reply
279
views
Computing the neighborhood graph in single cell pipeline
single-cell
knn
updated 7 months ago by
ATpoint
85k • written 7 months ago by
QX
▴ 60
0
votes
2
replies
452
views
Visualize and access gvcf/vcf files
genomics
vcf
updated 3 months ago by
venkat
▴ 10 • written 8 months ago by
QX
▴ 60
0
votes
2
replies
977
views
problem with importing mtx file in scanpy
scanpy
scRNAseq
9 months ago by
QX
▴ 60
1
vote
1
reply
467
views
Variant calling using HaplotypeCaller does not show #FILTER information
Variant-calling
GATK
HaplotypeCaller
WGS
updated 10 months ago by
Ram
44k • written 10 months ago by
QX
▴ 60
5
votes
2
replies
551
views
Execute R command on specific termimal
R
updated 11 months ago by
Ram
44k • written 11 months ago by
QX
▴ 60
3
votes
4
replies
1.1k
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
11 months ago by
QX
▴ 60
4
votes
2
replies
620
views
Normalization function in DEseq2
DEseq2
11 months ago by
QX
▴ 60
0
votes
0
replies
313
views
What is the difference between CNV binning and aligning to gene?
CNV
transcriptomics
12 months ago by
QX
▴ 60
2
votes
1
reply
502
views
Integrate proteomics and scRNA-seq datasets
scRNA-seq
omics
protemics
updated 14 months ago by
bk11
★ 3.0k • written 14 months ago by
QX
▴ 60
3
votes
4
replies
818
views
Integrate transcriptomics and CNV
CNV
omics
15 months ago by
QX
▴ 60
0
votes
0
replies
301
views
Normalization of NGS data to make CNV calls
CNV
Normalization
WGS
15 months ago by
QX
▴ 60
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