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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
47
views
How to remove unknown batch-batch effects from GEO datasets
GEO
unknown-batch-effects
just now by
2317711200
• 0
0
votes
0
replies
29
views
How to make "Custom annotation File" for GO analysis using TOPgo
enrichment
GO
analysis
TOPGO
3 hours ago by
hellokwmin
• 0
0
votes
0
replies
26
views
topGO error :KS elim test
KS
topGO
enrichment
-elim
analysis
4 hours ago by
Priya Rao
• 0
1
vote
1
reply
103
views
Best way to visualize .paf or .sam alignment to a fasta file
visualization
sam
fasta
paf
alignment
updated 10 hours ago by
GenoMax
127k • written 12 hours ago by
Mark
• 0
0
votes
0
replies
66
views
Problem when downloading dataset from ArrayExpress
Bioconductor
ArrayExpress
12 hours ago by
cogen859
• 0
0
votes
3
replies
122
views
using CITE-seq data to cluster single cells
clustering
cite-seq
k-means
10x
updated 1 hour ago by
ATpoint
70k • written 13 hours ago by
chi.delta
▴ 40
0
votes
0
replies
59
views
Extract cluster genes
fasta
extract
cluster
13 hours ago by
BATMAN
• 0
1
vote
2
replies
110
views
Analysing the Effect of a Drug on the Morphological Changes of a Cell Type
drug-effect
statistical-analysis
9 hours ago by
E-HR
• 0
3
votes
1
reply
95
views
Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq
ChIPseeker
GO
updated 13 hours ago by
Ram
38k • written 15 hours ago by
e.r.zakiev
▴ 30
0
votes
0
replies
63
views
Clustering method for CT values of two group
PCA
Clustering
bioconductor
R
15 hours ago by
Maria17
▴ 10
1
vote
1
reply
80
views
Integration of RNA seq data aligned to different reference genome versions
scRNA-seq
RNA-seq
updated 15 hours ago by
Ram
38k • written 16 hours ago by
susibing
▴ 20
0
votes
0
replies
59
views
UK BioBank HLA imputation
ukbb
hla
imputation
16 hours ago by
hla_help
• 0
0
votes
0
replies
61
views
ABSOLUTE for tumour purity with WES
tumour-purity
ABSOLUTE
WES
updated 17 hours ago by
Ram
38k • written 17 hours ago by
Cvlind
• 0
1
vote
4
replies
172
views
Suggestion for approaching multiple conditions scRNA-seq
scRNA-seq
16 hours ago by
Eisuan
▴ 20
2
votes
2
replies
142
views
STAR solo set parameters for scrna-seq
solo
STAR
21 hours ago by
t.ru
▴ 20
1
vote
3
replies
159
views
mpileup to sync file
AF
samtools
selection
vcf
popoolation
updated 23 hours ago by
Pierre Lindenbaum
153k • written 1 day ago by
qstefano
▴ 20
0
votes
1
reply
123
views
Quality control of Chip-seq data (NRF and PCB)
control
library
quality
PCB
Chip-seq
NRF
updated 16 hours ago by
Darked89
4.2k • written 1 day 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
19 hours ago by
andres.firrincieli
3.2k
1
vote
2
replies
179
views
Snakemake doesn't recognize output files even though they are created
python
Snakemake
13 hours ago by
DdogBoss
• 0
0
votes
0
replies
86
views
GO analysis using diamond blastp output
blastp
GO
analysis
Diamond
1 day ago by
hellokwmin
• 0
0
votes
0
replies
98
views
Diffbind: how to get raw read counts and normalized read counts
Diffbind
rawcount
1 day ago by
soda
▴ 40
0
votes
0
replies
98
views
Error at phase 4 when running GeMoMa (homology-based annotation)
Homology
GeMoMa
Annotation
Genome
1 day ago by
breannar
• 0
0
votes
5
replies
255
views
featureCounts problem in reading Gff
featureCounts
GFF
RNA-seq
updated 1 day ago by
Ram
38k • written 1 day ago by
Beatrice
• 0
0
votes
1
reply
125
views
Time change in expression vs time change in phenotype
RNA-Seq
DGE
DESeq2
1 day ago by
Ivan
• 0
0
votes
0
replies
79
views
How to perform a gsva assessing for the directonality of the genes.
gsva
1 day ago by
roybatty269
• 0
7
votes
7
replies
507
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 1 day ago by
Ram
38k • written 1 day ago by
Raygozak
★ 1.4k
0
votes
0
replies
77
views
calculation of calibration factors using impuation reference panel and ethnicity
GWAS
Calibration
factor
1 day ago by
parveenkayenat
• 0
1
vote
4
replies
223
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
21 hours ago by
Agamemnon
▴ 60
0
votes
0
replies
80
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftool
1 day ago by
Nai
▴ 50
0
votes
0
replies
115
views
How to export GWAS lists available in Open Targets database
GWAS
gene
openTargets
20 hours ago by
dzisis1986
▴ 60
0
votes
0
replies
114
views
Bcftools consensus generates mismatched consensus sequence
Consensus
sequence
1 day ago by
Duy
• 0
0
votes
0
replies
79
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
1 day ago by
audrey
• 0
0
votes
0
replies
100
views
Nucleotide substitution model and neighbor-joining tree
phylogeny
substitution
mega
neighbor-joining
modeltest
21 hours ago by
poecile.pal
▴ 50
0
votes
0
replies
99
views
Octopus advanced vcf guide: Example of overlapping vcf calls with *
vcf
spanning
alleles
octopus
1 day ago by
penington.j
• 0
0
votes
0
replies
117
views
how can we improve genome assembly levels ? from contig to complete using bioinformatics pipelines?
contig
genome
pipelines
assembly
updated 1 day ago by
Ram
38k • written 2 days ago by
vasudhapai
• 0
0
votes
0
replies
124
views
Link products to their genes
RNA-SEQ
GO
edgeR
2 days ago by
Pegasus
▴ 80
0
votes
0
replies
120
views
Trajectory analysis using Monocle3 with Seurat sub-clustering
scRNA-seq
Trajectory
Seurat
analysis
Monocle3
2 days ago by
joonhong kwon
▴ 40
0
votes
1
reply
172
views
Error parsing strand (?) from GFF line
assembly
updated 2 days ago by
cmdcolin
★ 2.9k • written 2 days ago by
hafiz.talhamalik
▴ 350
1
vote
0
replies
137
views
List of Ongoing and Planned Long Read Sequencing studies?
long-read-sequencing
third-generation
updated 2 days ago by
Ram
38k • written 2 days ago by
Vincent Laufer
★ 2.6k
0
votes
1
reply
159
views
SNP ID (rsID) to Chr no. and Position
Annotation
2 days ago by
Jewahir
• 0
0
votes
0
replies
125
views
how to plot distribution of SNPs across a set of genes based on distance between snp and gene
snp
genes
updated 2 days ago by
Ram
38k • written 2 days ago by
rheab1230
▴ 140
0
votes
0
replies
108
views
Reactome Species Comparison - analysis table
reactome
1 day ago by
a11msp
▴ 120
0
votes
1
reply
153
views
Using multimaping reads or unique reads on featurecounts?
featurecounts
HISAT2
updated 2 days ago by
GenoMax
127k • written 2 days ago by
omargmc.tak
• 0
0
votes
0
replies
98
views
How to import impute2.dosage files to analyse it in R (GWAS)
regression
GWAS
impute2
dosage
2 days ago by
Sebastian
• 0
0
votes
0
replies
98
views
Michigan Imputation server failed job
michigan-imputation-server
vcf
updated 2 days ago by
Ram
38k • written 2 days ago by
Najla
• 0
0
votes
0
replies
97
views
MD simulation error
MD
schrodinger
updated 2 days ago by
Ram
38k • written 2 days ago by
mixmatchey
• 0
0
votes
0
replies
104
views
File has zero value indivuals
Haploview
updated 2 days ago by
Ram
38k • written 2 days ago by
Nai
▴ 50
0
votes
6
replies
389
views
Kallisto bustools for scRNA-seq
Kallisto
updated 9 hours ago by
dsull
★ 4.0k • written 2 days ago by
t.ru
▴ 20
0
votes
0
replies
135
views
KEGGList Error in R
KEGGList
2 days ago by
GiV17
▴ 50
0
votes
0
replies
122
views
GATK VariantAnnotator -A PossibleDeNovo
VariantAnnotator
GATK
3 days ago by
zihanss
• 0
1,000 results • Page
1 of 20
Recent Votes
Easy way to run easily orthoMCL (Copy & paste)
Answer: Any tips in landing a bioinformatic job?
Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: What is the NCBI's definition of an "atypical genome"?
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Popular Question
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Bogdan
★ 1.3k
Popular Question
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pavelasquezv
▴ 50
Popular Question
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Anand Rao
▴ 550
Scholar
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3.2k
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Recent Replies
Answer: Extract data from Signac RegionMatrix?
by
Chironex
▴ 40
object@assays$ATAC@positionEnrichment$my_region_matrix and also object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job?
by
ATpoint
70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets
by
ATpoint
70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
Comment: using CITE-seq data to cluster single cells
by
ATpoint
70k
If it is really just two genes then why not just plotting logcounts of gene1 vs logcounts of gene2 as in a FACS scatter plot and see whethe…
Comment: How to remove unknown batch-batch effects from GEO datasets
by
2317711200
• 0
As a beginner, I hope to receive professional answers. If necessary, I can provide rewards and R code.
Answer: Align miRNA library (small RNA-seq) without trimming
by
ATpoint
70k
For miRNA you should trim the data to the actual expected miRNA length (20-something bp, I would need to look up the exact value). Reason i…
Comment: boxplot issue
by
ATpoint
70k
Please get used to make your question reproducible and precise, meaning provide example data and reduce code to a minimum.
Answer: Total No of Genes of GENCODE Release 43
by
ATpoint
70k
As I said, I assume that you are doing something on old/overwritten variables or a wrong GTF. This is how it is: a<-rtracklayer::i…
Answer: Any tips in landing a bioinformatic job?
by
Vincent Laufer
★ 2.6k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created? For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming
by
Paola
▴ 10
Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming
by
Ming Tommy Tang
★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression
by
afei
• 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa
by
rebeliscu
▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
by
cfos4698
▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking
by
Mensur Dlakic
★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
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