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940 results • Page
1 of 19
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Votes
Replies
0
votes
0
replies
22
views
How to find p-values for annotated methylated regions using methylkit and genomation
NGS
bioinformatics
pvalue
annotation
methylationarray
39 minutes ago by
Saransh
• 0
1
vote
1
reply
119
views
My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
R
ENSEMBL
DESeq2
updated 11 hours ago by
GenoMax
127k • written 12 hours ago by
rgomez
• 0
0
votes
0
replies
74
views
Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage?
SAM
BAM
Fields
bamCoverage
deeptools
12 hours ago by
Deep
• 0
0
votes
0
replies
92
views
HiC analysis in R
R
HiC
updated 15 hours ago by
Ram
38k • written 16 hours ago by
gitprohub4
• 0
0
votes
1
reply
113
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 1 hour ago by
pinheirofabiano
▴ 10 • written 18 hours ago by
reventropy2003
• 0
0
votes
1
reply
140
views
R package for functional enrichment and depletion analysis
enrichment
depletion
updated 15 hours ago by
rpolicastro
11k • written 19 hours ago by
lessismore
★ 1.3k
0
votes
2
replies
106
views
Gene family classification using RNA-seq data
RNA_seq
gene_expression
gene_family
10 minutes ago by
Dion
• 0
0
votes
0
replies
73
views
Seraut JackStrawplot PC1
jackstrawplot
Seurat
scRNAseq
PCA
updated 21 hours ago by
Ram
38k • written 22 hours ago by
miyeok
• 0
0
votes
1
reply
127
views
KEGG analysis in Hordeum
KEGG
vulgare
miRNA
transcripts
Hordeum
updated 19 hours ago by
GenoMax
127k • written 23 hours ago by
martta95
• 0
0
votes
1
reply
109
views
""ERROR:States for individual 0 are zero " when I using GLIMPSE2 for Imputation
PBWT
imputation
gene
GLIMPSE2
updated 20 hours ago by
4galaxy77
2.6k • written 23 hours ago by
2013677172
• 0
0
votes
0
replies
81
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
74
views
cell density scRNAseq
contourPlot
scRNAseq
1 day ago by
pingu77
▴ 10
0
votes
0
replies
63
views
fungal internal transcribed spacer metagenome (ITS)
METAGENOME
1 day ago by
Mahnoor
• 0
0
votes
0
replies
67
views
LD correlation matrix reference file, where can I find it?
ld
European
1000g
1 day ago by
Ger
• 0
0
votes
3
replies
187
views
How to deal with the probe id mapping to multiple gene ids?
match
microarray
affymetrix
probe
gene
7 hours ago by
dare_devil
★ 1.7k
0
votes
0
replies
89
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
91
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
115
views
Plink-association test
association
plink
case-control
covar
updated 23 hours ago by
Nicolas Rosewick
10k • written 1 day ago by
Viktor Messi
• 0
0
votes
0
replies
102
views
Single cell RNA expression level calculation ?
scanpy
scRNA
python
1 day ago by
Athens
• 0
0
votes
0
replies
112
views
EnhancedVolcano Labels
EnhancedVolcano
R
DESeq2
1 day ago by
GA
• 0
0
votes
0
replies
116
views
what is the impact of 10% contamination in bacterial growth experiment in downstream analysis?
bacterial
contamination
assay
experiment
1 day ago by
eli_bayat
▴ 80
0
votes
0
replies
122
views
Samtools sorting
Samtools
1 day ago by
Alireza
• 0
0
votes
1
reply
140
views
SKAT iniciation
SKAT
updated 1 day ago by
barslmn
★ 1.4k • written 1 day ago by
Ed
• 0
0
votes
1
reply
156
views
Difference between sratools and sratoolkit
sratools
fastq
sequencing
sratoolkit
sra
updated 23 hours ago by
GenoMax
127k • written 1 day ago by
hamarillo
▴ 10
0
votes
0
replies
114
views
alelle - specific CNA/LOH
cancer
CNV
genomics
LOH
CNA
1 day ago by
Bogdan
★ 1.3k
0
votes
4
replies
207
views
Problem in retrieving geo data sets
geo
1 day 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
163
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 2 days ago by
hellokwmin
• 0
0
votes
0
replies
99
views
topGO error: KS elim test
KS
topGO
enrichment-analysis
updated 1 day ago by
Ram
38k • written 2 days ago by
Priya Rao
• 0
1
vote
2
replies
194
views
Best way to visualize .paf or .sam alignment to a fasta file
visualization
sam
fasta
paf
alignment
updated 1 day ago by
colindaven
4.6k • written 2 days ago by
Mark
• 0
0
votes
0
replies
114
views
Problem when downloading dataset from ArrayExpress
Bioconductor
ArrayExpress
2 days ago by
cogen859
• 0
0
votes
3
replies
209
views
using CITE-seq data to cluster single cells
clustering
cite-seq
k-means
10x
updated 2 days ago by
ATpoint
71k • written 2 days ago by
chi.delta
▴ 40
0
votes
0
replies
104
views
Extract cluster genes
fasta
cluster
updated 1 day ago by
Ram
38k • written 2 days ago by
BATMAN
• 0
1
vote
2
replies
168
views
Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
drug-effect
statistical-analysis
2 days ago by
E-HR
• 0
3
votes
1
reply
146
views
Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq
ChIPseeker
GO
updated 2 days ago by
Ram
38k • written 2 days ago by
e.r.zakiev
▴ 30
0
votes
0
replies
108
views
Clustering method for CT values of two group
PCA
Clustering
bioconductor
R
2 days ago by
Maria17
▴ 10
1
vote
1
reply
133
views
Integration of RNA seq data aligned to different reference genome versions
scRNA-seq
RNA-seq
updated 2 days ago by
Ram
38k • written 2 days ago by
susibing
▴ 20
0
votes
0
replies
103
views
UK BioBank HLA imputation
ukbb
hla
imputation
2 days ago by
hla_help
• 0
0
votes
0
replies
113
views
ABSOLUTE for tumour purity with WES
tumour-purity
ABSOLUTE
WES
updated 2 days ago by
Ram
38k • written 2 days ago by
Cvlind
• 0
1
vote
4
replies
218
views
Suggestion for approaching multiple conditions scRNA-seq
scRNA-seq
2 days ago by
Eisuan
▴ 20
1
vote
3
replies
195
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
1
reply
143
views
Quality control of Chip-seq data (NRF and PCB)
control
library
quality
PCB
Chip-seq
NRF
updated 2 days ago by
Darked89
4.2k • written 3 days ago by
michelafrancesconi9
• 0
0
votes
2
replies
2.7k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing
guppy
2 days ago by
andres.firrincieli
3.2k
1
vote
4
replies
313
views
Snakemake doesn't recognize output files even though they are created
python
Snakemake
13 hours ago by
DdogBoss
• 0
0
votes
0
replies
95
views
GO analysis using diamond blastp output
blastp
GO
analysis
Diamond
3 days ago by
hellokwmin
• 0
0
votes
0
replies
108
views
Error at phase 4 when running GeMoMa (homology-based annotation)
Homology
GeMoMa
Annotation
Genome
3 days ago by
breannar
• 0
0
votes
5
replies
273
views
featureCounts problem in reading Gff
featureCounts
GFF
RNA-seq
updated 3 days ago by
Ram
38k • written 3 days ago by
Beatrice
• 0
0
votes
1
reply
138
views
Time change in expression vs time change in phenotype
RNA-Seq
DGE
DESeq2
3 days ago by
Ivan
• 0
0
votes
0
replies
86
views
How to perform a gsva assessing for the directonality of the genes.
gsva
3 days ago by
roybatty269
• 0
7
votes
7
replies
528
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 3 days ago by
Ram
38k • written 3 days ago by
Raygozak
★ 1.4k
940 results • Page
1 of 19
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Awards •
All
Popular Question
to
moshi
▴ 90
Popular Question
to
optimistsso4co3
▴ 100
Popular Question
to
zhou_1228
• 0
Teacher
to
GenoMax
127k
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Mensur Dlakic
★ 23k
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Pierre Lindenbaum
153k
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lessismore
★ 1.3k
Recent Replies
Comment: pyCirclize - Circular visualization in Python
by
moshi
▴ 90
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…
Answer: 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…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
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