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133 results • Page
2 of 3
Sort: replies
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Views
Votes
Replies
0
votes
1
reply
126
views
KEGG analysis in Hordeum
KEGG
vulgare
miRNA
transcripts
Hordeum
updated 18 hours ago by
GenoMax
127k • written 22 hours ago by
martta95
• 0
0
votes
1
reply
107
views
TCGA-BRCA tissue and RNAseq problem
NIH
RNAseq
GDC
TCGA-BRCA
updated 1 hour ago by
pinheirofabiano
▴ 10 • written 17 hours ago by
reventropy2003
• 0
3
votes
1
reply
2.3k
views
Noncoding Rna Mapping
non-coding-RNA
updated 4 days ago by
Ram
38k • written 9.8 years ago by
Honey
▴ 200
1
vote
1
reply
244
views
Libraries with different size in the same MiniSeq cartridge
Illumina
MiniSeq
UMI
updated 4 days ago by
Ram
38k • written 11 months ago by
MH85
• 0
0
votes
1
reply
114
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
2
votes
1
reply
2.1k
views
Question about PLINK allelic scoring (PRS)
plink
PRS
updated 2 days ago by
Ram
38k • written 4.6 years ago by
wonseok.cchoi
• 0
0
votes
1
reply
595
views
Insert size historgram from Picard for Illumina paried end 150 bp: FR, TANDEM, and both
Illumina
bam
insert-size
updated 4 days ago by
Ram
38k • written 16 months ago by
robertwhbaldwin
• 0
0
votes
1
reply
177
views
Tell me about making a transcriptome model of a specific tissue.
model
transcriptome
updated 6 days ago by
ATpoint
71k • written 6 days ago by
Soliloquy
▴ 10
0
votes
1
reply
155
views
Difference between sratools and sratoolkit
sratools
fastq
sequencing
sratoolkit
sra
updated 22 hours ago by
GenoMax
127k • written 1 day ago by
hamarillo
▴ 10
0
votes
1
reply
98
views
Gene family classification using RNA-seq data
RNA_seq
gene_expression
gene_family
updated 19 hours ago by
jv
★ 1.0k • written 20 hours ago by
Dion
• 0
0
votes
1
reply
140
views
SKAT iniciation
SKAT
updated 23 hours ago by
barslmn
★ 1.4k • written 1 day ago by
Ed
• 0
4
votes
1
reply
2.9k
views
How Do I Get A Gff Files Or Make My Own For A Bacteriophage?
gtf
gff
updated 4 days ago by
Ram
38k • written 10.0 years ago by
joaslucas
▴ 90
0
votes
1
reply
159
views
Using multimaping reads or unique reads on featurecounts?
featurecounts
HISAT2
updated 4 days ago by
GenoMax
127k • written 4 days ago by
omargmc.tak
• 0
0
votes
1
reply
137
views
R package for functional enrichment and depletion analysis
enrichment
depletion
updated 14 hours ago by
rpolicastro
11k • written 18 hours ago by
lessismore
★ 1.3k
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
1
reply
107
views
""ERROR:States for individual 0 are zero " when I using GLIMPSE2 for Imputation
PBWT
imputation
gene
GLIMPSE2
updated 19 hours ago by
4galaxy77
2.6k • written 22 hours ago by
2013677172
• 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
114
views
Reactome Species Comparison - analysis table
reactome
3 days ago by
a11msp
▴ 120
0
votes
0
replies
165
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta
analysis
GWAS
METAL
updated 6 days ago by
GenoMax
127k • written 6 days ago by
ymberzal
• 0
0
votes
0
replies
587
views
Reducing block size used in Spark versions of GATK tools
gatk
spark
updated 4 days ago by
Ram
38k • written 3.6 years ago by
aalith
▴ 10
0
votes
0
replies
217
views
Estimating the number of genomes in a metagenome
metagenomics
genome
gene
single-copy
updated 4 days ago by
Ram
38k • written 8 months ago by
pfchuckran
▴ 30
0
votes
0
replies
3.3k
views
Window size and strigency in Dotplot
dot-plot
BLAST
updated 1 day ago by
Ram
38k • written 7.5 years ago by
D H
▴ 10
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
0
votes
0
replies
2.0k
views
Target Info File And Pooled Info File For Syzygy
syzygy
updated 4 days ago by
Ram
38k • written 9.5 years ago by
sandhya0888
• 0
0
votes
0
replies
1.0k
views
Getting started with miRNA prediction
miRNA
updated 19 hours ago by
Ram
38k • written 7.4 years ago by
Nuria_bl
▴ 10
0
votes
0
replies
1.6k
views
Bioinformatics for algae research
genomics
algae
updated 1 day ago by
Ram
38k • written 7.4 years ago by
Arindam Ghosh
▴ 470
0
votes
0
replies
139
views
KEGGList Error in R
KEGGList
5 days ago by
GiV17
▴ 50
0
votes
0
replies
188
views
How to sort graph based on fold change and instead of activated and suppressed, how to add up and downregulated in graph header?
clusterprofiler
5 days ago by
sharmatina189059
▴ 110
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
83
views
Is there a function to get the number of aligned sites between pairs of sequences in a multiple sequence alignment in R?
msa
R
4 days ago by
audrey
• 0
0
votes
0
replies
101
views
How to import impute2.dosage files to analyse it in R (GWAS)
regression
GWAS
impute2
dosage
4 days ago by
Sebastian
• 0
0
votes
0
replies
101
views
Single cell RNA expression level calculation ?
scanpy
scRNA
python
1 day ago by
Athens
• 0
0
votes
0
replies
100
views
MD simulation error
MD
schrodinger
updated 4 days ago by
Ram
38k • written 4 days ago by
mixmatchey
• 0
0
votes
0
replies
1.1k
views
Does it make sense to limit insert size when mapping on transcriptome?
RNA-seq
transcriptome
updated 4 days ago by
Ram
38k • written 5.5 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
120
views
Samtools sorting
Samtools
1 day ago by
Alireza
• 0
0
votes
0
replies
108
views
File has zero value indivuals
Haploview
updated 4 days ago by
Ram
38k • written 4 days ago by
Nai
▴ 50
0
votes
0
replies
111
views
EnhancedVolcano Labels
EnhancedVolcano
R
DESeq2
1 day ago by
GA
• 0
0
votes
0
replies
124
views
GATK VariantAnnotator -A PossibleDeNovo
VariantAnnotator
GATK
5 days ago by
zihanss
• 0
0
votes
0
replies
82
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftool
3 days ago by
Nai
▴ 50
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
0
votes
0
replies
89
views
HiC analysis in R
R
HiC
updated 14 hours ago by
Ram
38k • written 15 hours ago by
gitprohub4
• 0
0
votes
0
replies
1.6k
views
constructing smoothed species area curves with different sample sizes?
area-curve
species
sample-size
updated 4 days ago by
Ram
38k • written 7.0 years ago by
horchler
• 0
0
votes
0
replies
217
views
a question about genomescope2
genome
updated 4 days ago by
Ram
38k • written 14 months ago by
542042930
• 0
0
votes
0
replies
147
views
Best method for downstream GSEA to adjust the gene set size to 500 from a 58,000 mark RNA-seq dataset
gene-set
GSEA
updated 4 days ago by
Ram
38k • written 12 months ago by
RZ
• 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
0
votes
0
replies
156
views
Extract/include transcript list from GAGE analysis result
RNAseq
GAGE
4 days ago by
farzaneafzali
▴ 70
0
votes
0
replies
72
views
Seraut JackStrawplot PC1
jackstrawplot
Seurat
scRNAseq
PCA
updated 20 hours ago by
Ram
38k • written 21 hours ago by
miyeok
• 0
0
votes
0
replies
285
views
How to deal with differences in sample size for metagenomic diversity based on abundance?
metagenomics
sample-size
updated 4 days ago by
Ram
38k • written 19 months ago by
goatsrunfaster
▴ 50
1
vote
0
replies
166
views
Minimap2 giving opposite strand orientation than Pychopper
nanopore
Pychopper
Minimap2
6 days ago by
vanda.gaonach-lovejoy
▴ 10
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
133 results • Page
2 of 3
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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Popular Question
to
zhou_1228
• 0
Teacher
to
GenoMax
127k
Scholar
to
Mensur Dlakic
★ 23k
Teacher
to
Pierre Lindenbaum
153k
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lessismore
★ 1.3k
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onca
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coleman_jonathan
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Recent Replies
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…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
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