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930 results • Page
1 of 19
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0
votes
0
replies
1
view
Entrez direct does not give output sometimes
entrez_direct
entrez
just now by
fafad046
• 0
0
votes
0
replies
5
views
how to add TCGA CNV as covariate for matrixeqtl
covariate
matrixeqtl
CNV
33 minutes ago by
Binghong
▴ 20
0
votes
0
replies
13
views
Process mining in bioinformatics
processmining
51 minutes ago by
Cygi
• 0
0
votes
0
replies
12
views
Getting an "double free or corruption (out)" error when running wigToBigWig
wigToBigwig
59 minutes ago by
rls_08
▴ 40
0
votes
0
replies
8
views
Get Count matrix of geodatasets
geo
R
1 hour ago by
anasjamshed
▴ 120
0
votes
0
replies
10
views
Differences between GSVA and GSEA?
gsea
genome
genetics
gene
gsva
1 hour ago by
DS
▴ 20
0
votes
0
replies
28
views
Recommendations on Public Linux server for academics purposes
server
linux
rna-seq
2 hours ago by
Ant
• 0
0
votes
0
replies
65
views
Any straightforward way to re-bin a bigWig file?
bigwig
10 hours ago by
rls_08
▴ 40
0
votes
0
replies
103
views
How to get BEAGLE files from VCF with angsd?
angsd
vcf
populationgenetics
beagle
pcangsd
16 hours ago by
Begonia_pavonina
▴ 90
0
votes
0
replies
135
views
How to find p-values for annotated methylated regions using methylkit and genomation
NGS
bioinformatics
pvalue
annotation
methylationarray
17 hours ago by
Saransh
• 0
0
votes
0
replies
145
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
SAM
BAM
Fields
bamCoverage
deeptools
1 day ago by
Deep
• 0
0
votes
0
replies
136
views
HiC analysis in R
R
HiC
updated 1 day ago by
Ram
38k • written 1 day ago by
gitprohub4
• 0
0
votes
1
reply
232
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 19 hours ago by
pinheirofabiano
▴ 10 • written 1 day ago by
reventropy2003
• 0
0
votes
2
replies
213
views
Gene family classification using RNA-seq data
RNA_seq
gene_expression
gene_family
17 hours ago by
Dion
• 0
0
votes
0
replies
103
views
Seraut JackStrawplot PC1
jackstrawplot
Seurat
scRNAseq
PCA
updated 1 day ago by
Ram
38k • written 1 day ago by
miyeok
• 0
0
votes
1
reply
161
views
KEGG analysis in Hordeum
KEGG
vulgare
miRNA
transcripts
Hordeum
updated 1 day ago by
GenoMax
127k • written 1 day ago by
martta95
• 0
0
votes
1
reply
139
views
""ERROR:States for individual 0 are zero " when I using GLIMPSE2 for Imputation
PBWT
imputation
gene
GLIMPSE2
updated 1 day ago by
4galaxy77
2.6k • written 1 day ago by
2013677172
• 0
0
votes
0
replies
113
views
How to interpret LASSO results for creating gene signature ?
Microarray
KM
OS
plot
1 day ago by
prithvi.mastermind
▴ 50
0
votes
0
replies
104
views
cell density scRNAseq
contourPlot
scRNAseq
1 day ago by
pingu77
▴ 10
0
votes
0
replies
91
views
fungal internal transcribed spacer metagenome (ITS)
METAGENOME
1 day ago by
Mahnoor
• 0
0
votes
0
replies
99
views
LD correlation matrix reference file, where can I find it?
ld
European
1000g
1 day ago by
Ger
• 0
0
votes
3
replies
275
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
1 day ago by
dare_devil
★ 1.7k
0
votes
0
replies
123
views
kraken2 - unmapped sequences during the first step of building the database #708
metagenomics
kraken2
taxonomy
kraken
linux
1 day ago by
aziznasr1920
• 0
0
votes
0
replies
119
views
UCSC Xena browser subgroup DNA Methylation data by beta value for a specific probe
Methylation
DNA
UCSC
Xena
probe
1 day ago by
smbc
• 0
0
votes
1
reply
149
views
Plink-association test
association
plink
case-control
covar
updated 1 day ago by
Nicolas Rosewick
10k • written 1 day ago by
Viktor Messi
• 0
0
votes
0
replies
134
views
Single cell RNA expression level calculation ?
scanpy
scRNA
python
2 days ago by
Athens
• 0
0
votes
0
replies
141
views
EnhancedVolcano Labels
EnhancedVolcano
R
DESeq2
2 days ago by
GA
• 0
0
votes
0
replies
143
views
what is the impact of 10% contamination in bacterial growth experiment in downstream analysis?
bacterial
contamination
assay
experiment
2 days ago by
eli_bayat
▴ 80
0
votes
0
replies
152
views
Samtools sorting
Samtools
2 days ago by
Alireza
• 0
0
votes
1
reply
172
views
SKAT iniciation
SKAT
updated 1 day ago by
barslmn
★ 1.4k • written 2 days ago by
Ed
• 0
0
votes
1
reply
186
views
Difference between sratools and sratoolkit
sratools
fastq
sequencing
sratoolkit
sra
updated 1 day ago by
GenoMax
127k • written 2 days ago by
hamarillo
▴ 10
0
votes
0
replies
141
views
alelle - specific CNA/LOH
cancer
CNV
genomics
LOH
CNA
2 days ago by
Bogdan
★ 1.3k
0
votes
4
replies
221
views
Problem in retrieving geo data sets
geo
2 days ago by
anasjamshed
▴ 120
0
votes
0
replies
97
views
Use GraphQL to query miltiple rsIDs from GWAS study in Open Targets
OpenTargets
GWAS
GraphQL
2 days ago by
dzisis1986
▴ 60
0
votes
1
reply
164
views
How to make "Custom annotation File" for GO analysis using TOPgo
enrichment
GO
analysis
TOPGO
updated 2 days ago by
Shred
★ 1.1k • written 3 days ago by
hellokwmin
• 0
0
votes
0
replies
99
views
topGO error: KS elim test
KS
topGO
enrichment-analysis
updated 2 days ago by
Ram
38k • written 3 days ago by
Priya Rao
• 0
1
vote
2
replies
196
views
Best way to visualize .paf or .sam alignment to a fasta file
visualization
sam
fasta
paf
alignment
updated 2 days ago by
colindaven
4.7k • written 3 days ago by
Mark
• 0
0
votes
0
replies
115
views
Problem when downloading dataset from ArrayExpress
Bioconductor
ArrayExpress
3 days ago by
cogen859
• 0
0
votes
3
replies
214
views
using CITE-seq data to cluster single cells
clustering
cite-seq
k-means
10x
updated 2 days ago by
ATpoint
71k • written 3 days ago by
chi.delta
▴ 40
0
votes
0
replies
105
views
Extract cluster genes
fasta
cluster
updated 2 days ago by
Ram
38k • written 3 days ago by
BATMAN
• 0
1
vote
2
replies
173
views
Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
drug-effect
statistical-analysis
3 days ago by
E-HR
• 0
3
votes
1
reply
148
views
Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq
ChIPseeker
GO
updated 3 days ago by
Ram
38k • written 3 days ago by
e.r.zakiev
▴ 30
0
votes
0
replies
109
views
Clustering method for CT values of two group
PCA
Clustering
bioconductor
R
3 days ago by
Maria17
▴ 10
1
vote
1
reply
134
views
Integration of RNA seq data aligned to different reference genome versions
scRNA-seq
RNA-seq
updated 3 days ago by
Ram
38k • written 3 days ago by
susibing
▴ 20
0
votes
0
replies
105
views
UK BioBank HLA imputation
ukbb
hla
imputation
3 days ago by
hla_help
• 0
0
votes
0
replies
115
views
ABSOLUTE for tumour purity with WES
tumour-purity
ABSOLUTE
WES
updated 3 days ago by
Ram
38k • written 3 days ago by
Cvlind
• 0
1
vote
4
replies
225
views
Suggestion for approaching multiple conditions scRNA-seq
scRNA-seq
3 days ago by
Eisuan
▴ 20
1
vote
3
replies
200
views
mpileup to sync file
AF
samtools
selection
vcf
popoolation
updated 3 days ago by
Pierre Lindenbaum
153k • written 3 days ago by
qstefano
▴ 20
0
votes
2
replies
221
views
Quality control of Chip-seq data (NRF and PCB)
control
library
quality
PCB
Chip-seq
NRF
15 hours ago by
michelafrancesconi9
• 0
0
votes
2
replies
2.8k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing
guppy
3 days ago by
andres.firrincieli
3.2k
930 results • Page
1 of 19
Recent Votes
Answer: how can i filter a sam file from a paf file
Answer: Align miRNA library (small RNA-seq) without trimming
Answer: Snakemake workflow for trimmomatic
C: Adjust for covariates
Comment: syntax errors when running part3 all-against-all
Picard LiftOver rejecting all Variants
Comment: pyCirclize - Circular visualization in Python
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Recent Awards •
All
Popular Question
to
anasjamshed
▴ 120
Teacher
to
Papyrus
★ 2.4k
Popular Question
to
smrutimayipanda
▴ 20
Popular Question
to
mohammedtoufiq91
▴ 210
Popular Question
to
mnmalash
• 0
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Trombone Engineer
• 0
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moshi
▴ 110
Recent Replies
Comment: Diffbind dba.count doesn't give FRiP score
by
gyspace
• 0
I found your email in https://bioinfotraining.bio.cam.ac.uk/staff/rory-stark-phd, is the email right? I sent a google drive link to you. If…
Comment: how can i filter a sam file from a paf file
by
colindaven
4.6k
Just save yourself a lot of pain and learn to filter the sam/bam file efficiently. It is much more of a widespread standard than PAF.
Comment: Snakemake workflow for trimmomatic
by
GenoMax
127k
Please accept this answer (green check mark) to provide closure to this thread.
Comment: syntax errors when running part3 all-against-all
by
Sofia
• 0
When I started with the gz all-vs-all files for CHICK and ANOCA and started oma, everything ran fine, I got output. Then, in the same direc…
Comment: Quality control of Chip-seq data (NRF and PCB)
by
michelafrancesconi9
• 0
Can you explain me better? Because for the NRF I do : a) samtools view -c .bam b)samtools view -c -F 260 .bam then b/a and as a bam fi…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for responding so quickly - this works perfectly!
Comment: pyCirclize - Circular visualization in Python
by
moshi
▴ 110
Please install Biopython with v1.80 or higher. If biopython>=1.80, there should be no errors.
Comment: Gene family classification using RNA-seq data
by
Dion
• 0
well, I have been given the task to retrieve gene family/categorization. I found sveral papers on family classification, but no actual pack…
Comment: pyCirclize - Circular visualization in Python
by
karenkvn
▴ 40
Thank you for this wonderful programme! I am plotting a bacterial chromosome and find that when I plot the NC_000913 chromosome using the e…
Comment: SKAT in R
by
Eliza
▴ 20
@acvill can you sujjest maybe pther tools , methods for this ? ( also for every SNP i have data how many patients had the hetro/homozygous…
Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Comment: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
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