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0
votes
3
replies
434
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DEseq2 with different designs matrix
DEseq2
5 weeks ago by
QX
▴ 60
0
votes
0
replies
137
views
Different position for same gene using annotatePeak from ChIPseeker
ChIPseeker
ATACseq
6 weeks ago by
QX
▴ 60
0
votes
0
replies
140
views
plotHeatmap from deeptools explain
atac-seq
6 weeks ago by
QX
▴ 60
5
votes
4
replies
472
views
difference between macs2 callpeak using bam and bed file
macs2
atac-seq
7 weeks ago by
QX
▴ 60
2
votes
5
replies
429
views
call peak for all replicates in all conditions using macs2
macs2
ATACseq
updated 7 weeks ago by
zau saa
▴ 150 • written 7 weeks ago by
QX
▴ 60
1
vote
4
replies
360
views
trimming 151bp to shorter k-mer in ATAC-seq analysis
ATAC-seq
7 weeks ago by
QX
▴ 60
3
votes
6
replies
560
views
which bed file should be used for deeptools computeMatrix
atac-seq
deeptools
updated 8 weeks ago by
Ming Tommy Tang
★ 4.3k • written 8 weeks ago by
QX
▴ 60
0
votes
0
replies
165
views
reference-point setting from computeMatrix
ATACseq
9 weeks ago by
QX
▴ 60
0
votes
0
replies
132
views
which distance used for kmeans in deeptools plotHeatmap
atac
deeptools
9 weeks ago by
QX
▴ 60
1
vote
1
reply
221
views
merge replicate for bigWig files from macs2 peak calling
ATAC-seq
updated 9 weeks ago by
ATpoint
85k • written 9 weeks ago by
QX
▴ 60
4
votes
4
replies
321
views
MACS2 for multiple conditions in ATACseq analysis
mac2
10 weeks ago by
QX
▴ 60
4
votes
4
replies
530
views
Increase the memory and core usage of R
R
updated 10 weeks ago by
Mensur Dlakic
★ 28k • written 10 weeks ago by
QX
▴ 60
3
votes
2
replies
389
views
is that statistical correct to use DEseq2 for proteomics data
proteomics
DEseq2
updated 10 weeks ago by
ATpoint
85k • written 10 weeks ago by
QX
▴ 60
4
votes
8
replies
525
views
featureCounts output
macs2
featureCounts
updated 10 weeks ago by
rfran010
★ 1.3k • written 11 weeks ago by
QX
▴ 60
2
votes
6
replies
465
views
input for gatk VariantAnnotator --dbsnp
VariantAnnotator
gatk
updated 12 weeks ago by
GenoMax
146k • written 12 weeks ago by
QX
▴ 60
5
votes
5
replies
470
views
best way to submit hpc job using snakemake
snakemake
3 months ago by
QX
▴ 60
1
vote
3
replies
312
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
304
views
how to colorize snakemake editing text
snakemake
updated 3 months ago by
Michael
55k • written 3 months ago by
QX
▴ 60
3
votes
5
replies
580
views
Calling variants/SNP for single-cell RNA-seq data
SNP
scRNAseq
updated 6 weeks ago by
yura.grabovska
▴ 520 • written 3 months ago by
QX
▴ 60
2
votes
1
reply
304
views
Split the fastqc file base on barcode
fastq
updated 3 months ago by
GenoMax
146k • written 3 months ago by
QX
▴ 60
2
votes
3
replies
404
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
532
views
chIP-seq vs ATACseq analysis
ATACseq
4 months ago by
QX
▴ 60
0
votes
1
reply
374
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
477
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
271
views
Trimming from 151bp to 65bp
sequencing
data
updated 4 months ago by
GenoMax
146k • written 4 months ago by
QX
▴ 60
5
votes
11
replies
665
views
6 follow
Asking for parallel jobs setting on HPC when analyzing sequencing data
HPC
parallel
updated 4 months ago by
Darked89
4.7k • written 4 months ago by
QX
▴ 60
4
votes
2
replies
415
views
cannot conda install macs3 on linux
atac
macs3
4 months ago by
QX
▴ 60
3
votes
5
replies
658
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 4 months ago by
Pierre Lindenbaum
164k • written 4 months ago by
QX
▴ 60
3
votes
3
replies
444
views
Unexpected read length from NGS
NGS
Illumina
4 months ago by
QX
▴ 60
3
votes
4
replies
629
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
5 months ago by
QX
▴ 60
0
votes
0
replies
185
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
5 months ago by
QX
▴ 60
0
votes
0
replies
167
views
NicheNet cell-cell communication analysis outcome
nichenet
scRNA-seq
6 months ago by
QX
▴ 60
2
votes
3
replies
567
views
Annotate genes from gtf file to vcf file
gtf
genomics
vcf
6 months ago by
QX
▴ 60
0
votes
1
reply
295
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 6 months ago by
ATpoint
85k • written 6 months ago by
QX
▴ 60
0
votes
1
reply
276
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
265
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
425
views
Visualize and access gvcf/vcf files
genomics
vcf
updated 3 months ago by
venkat
▴ 10 • written 7 months ago by
QX
▴ 60
0
votes
2
replies
928
views
problem with importing mtx file in scanpy
scanpy
scRNAseq
9 months ago by
QX
▴ 60
1
vote
1
reply
455
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
542
views
Execute R command on specific termimal
R
updated 10 months ago by
Ram
44k • written 10 months ago by
QX
▴ 60
3
votes
4
replies
1.1k
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
10 months ago by
QX
▴ 60
4
votes
2
replies
602
views
Normalization function in DEseq2
DEseq2
10 months ago by
QX
▴ 60
0
votes
0
replies
305
views
What is the difference between CNV binning and aligning to gene?
CNV
transcriptomics
11 months ago by
QX
▴ 60
2
votes
1
reply
497
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
806
views
Integrate transcriptomics and CNV
CNV
omics
14 months ago by
QX
▴ 60
0
votes
0
replies
295
views
Normalization of NGS data to make CNV calls
CNV
Normalization
WGS
14 months ago by
QX
▴ 60
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