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questions
0
votes
0
replies
118
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
7 days ago by
Bogdan
★ 1.4k
0
votes
0
replies
198
views
Copy Number Alteration and Loss or Heterozygosity
LOH
CNA
copy-number
updated 3 months ago by
Ram
40k • written 3 months ago by
Bogdan
★ 1.4k
2
votes
3
replies
621
views
fitting a copy number profile to know CNV signatures
CNV
copy
number
LOH
CNA
updated 5 months ago by
LauferVA
3.7k • written 5 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
220
views
allelic copy number variation
LOH
CNA
CNV
copy-number
updated 5 months ago by
Ram
40k • written 5 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
240
views
alelle - specific CNA/LOH
cancer
CNV
genomics
LOH
CNA
6 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
210
views
network alignment and network regression
network
7 months ago by
Bogdan
★ 1.4k
1
vote
0
replies
402
views
CNA/LOH caller on WGS data and chromosomal instability index
CNA
CNV
9 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
381
views
downloading the VCF files of CCLE project (or cancer genomics WGS)
cancer
genomics
WGS
CCLE
VCF
9 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
274
views
packages to detect chromoanagenesis phenomena in germline or cancer genomes
ShatterProof
9 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
191
views
clustering of genome segments
cancer
genomics
epigenetics
10 months ago by
Bogdan
★ 1.4k
3
votes
2
replies
531
views
wig2bed and counting the reads in the peaks
bedtools
ChIP-seq
deeptools
bedops
updated 3 months ago by
Ram
40k • written 11 months ago by
Bogdan
★ 1.4k
2
votes
1
reply
676
views
normalize and compare bigwig files
bigwig
updated 12 months ago by
Matthias Zepper
4.1k • written 12 months ago by
Bogdan
★ 1.4k
0
votes
1
reply
490
views
calling peaks in ChIP-seq datasets from bedgraph files
ChIP-seq
MACS2
updated 12 months ago by
Marco Pannone
▴ 760 • written 12 months ago by
Bogdan
★ 1.4k
0
votes
11
replies
1.5k
views
paired-end reads, idxstats, and samtools and grep
samtools
updated 12 months ago by
LauferVA
3.7k • written 13 months ago by
Bogdan
★ 1.4k
5
votes
8
replies
1.4k
views
converting bedgraph to bigwig by not using ucsc tools
bedgraph
bigwig
13 months ago by
Bogdan
★ 1.4k
3
votes
3
replies
796
views
CWL and Arvados
CWL
workflow
manager
13 months ago by
Bogdan
★ 1.4k
0
votes
1
reply
501
views
SNV, CNA, SV
SV
CNA
SNV
updated 13 months ago by
LauferVA
3.7k • written 13 months ago by
Bogdan
★ 1.4k
2
votes
1
reply
340
views
extracting sequences from a bam file
bam
updated 13 months ago by
LChart
3.4k • written 13 months ago by
Bogdan
★ 1.4k
1
vote
3
replies
853
views
comparisons between 2 ChIP-seq datasets
ChIP-seq
updated 16 months ago by
ATpoint
77k • written 16 months ago by
Bogdan
★ 1.4k
4
votes
3
replies
1.3k
views
computing chromothripsis on cancer genomes
snp
cnv
sv
cancer
updated 16 months ago by
Thind amarinder
▴ 330 • written 5.2 years ago by
Bogdan
★ 1.4k
0
votes
2
replies
466
views
browser to visualize single cell data
scATAC-seq
updated 16 months ago by
lieven.sterck
14k • written 16 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
240
views
HIC databases
Hi-C
17 months ago by
Bogdan
★ 1.4k
2
votes
1
reply
459
views
scATAC-seq
scATAC-seq
18 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
314
views
ssvQC
ssvQC
19 months ago by
Bogdan
★ 1.4k
0
votes
5
replies
1.1k
views
saving png images and X11
scripting
saving
images
and
16 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
381
views
HOMER on AWS
HOMER
19 months ago by
Bogdan
★ 1.4k
0
votes
1
reply
545
views
compare the background levels in two chip-seq experiments
ChIPseq
updated 19 months ago by
seidel
11k • written 19 months ago by
Bogdan
★ 1.4k
0
votes
2
replies
467
views
interchromosomal interactions and 4C
4C
19 months ago by
Bogdan
★ 1.4k
1
vote
4
replies
651
views
compare ChIP-seq datasets in two cell lines
ChIP-seq
20 months ago by
Bogdan
★ 1.4k
19
votes
10
replies
11k
views
7 follow
workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
pipeline
language
updated 17 months ago by
dariober
14k • written 4.9 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
530
views
4C packages
4C
updated 20 months ago by
LauferVA
3.7k • written 20 months ago by
Bogdan
★ 1.4k
5
votes
4
replies
1.7k
views
6 follow
bioinformatics pipelines on GCP or AWS
RNA-seq
google
ChIP-seq
cloud
updated 18 months ago by
LauferVA
3.7k • written 2.0 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
744
views
shiny apps for DEseq2, edgeR, limma
shiny
limma
DEseq2
edgeR
updated 21 months ago by
tbkuipers
▴ 30 • written 21 months ago by
Bogdan
★ 1.4k
1
vote
1
reply
2.1k
views
heatmap of genes pseudotime in monocle3
monocle3
and
monocle2
11 months ago by
Bogdan
★ 1.4k
0
votes
2
replies
949
views
monocle3 and spData
monocle3
23 months ago by
Bogdan
★ 1.4k
0
votes
0
replies
654
views
convert monocle3 into monocle2 cds
monocle
23 months ago by
Bogdan
★ 1.4k
1
vote
1
reply
400
views
scanning sequences or promoter sequences with specific motifs
motifs
updated 2.1 years ago by
cpad0112
21k • written 2.1 years ago by
Bogdan
★ 1.4k
0
votes
4
replies
834
views
batch correction in ChIp-seq data
batch
ChIP-seq
updated 2.1 years ago by
rpolicastro
12k • written 2.1 years ago by
Bogdan
★ 1.4k
1
vote
3
replies
884
views
extracting a gene from a gmt file
gmt
pathway
updated 10 months ago by
Ram
40k • written 2.1 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
649
views
downloading fastq files from galaxy
galaxy
updated 2.3 years ago by
swbarnes2
13k • written 2.3 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
517
views
about the batch correction and integration and normalization of scRNA-seq data
normalization
scRNA-seq
2.4 years ago by
Bogdan
★ 1.4k
6
votes
3
replies
980
views
recent Hi-C databases
hi-C
4C
3C
updated 2.4 years ago by
kalavattam
▴ 190 • written 2.7 years ago by
Bogdan
★ 1.4k
3
votes
1
reply
609
views
HI-C analysis in the cloud environment
HI-C
updated 2.5 years ago by
kalavattam
▴ 190 • written 2.6 years ago by
Bogdan
★ 1.4k
0
votes
3
replies
724
views
to annotate BEDPE files
bedtools
annotate
updated 5 days ago by
Lhl
▴ 760 • written 2.6 years ago by
Bogdan
★ 1.4k
0
votes
2
replies
392
views
a simple question about file permissions
SLURM cluster
operating system
2.6 years ago by
Bogdan
★ 1.4k
0
votes
1
reply
875
views
CUT&TAG and CUT&RUN
ChIP-Seq
updated 2.7 years ago by
i.sudbery
17k • written 2.7 years ago by
Bogdan
★ 1.4k
1
vote
5
replies
2.0k
views
scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics
scRNA-seq
updated 2.7 years ago by
VolEr
▴ 40 • written 2.9 years ago by
Bogdan
★ 1.4k
0
votes
6
replies
932
views
visualize RNA secondary/tertiary structure, and overlay the primary sequence
RNA
RNA structure
visualization
2.8 years ago by
Bogdan
★ 1.4k
5
votes
11
replies
4.5k
views
filtering the somatic variants
SNP
snp
updated 2.8 years ago by
zhoujun.nmu
• 0 • written 7.5 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
503
views
database of human mRNA structures
RNA
2.8 years ago by
Bogdan
★ 1.4k
153 results • Page
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