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194 results • Page
3 of 4
Sort: Views
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Views
Votes
Replies
1
vote
1
reply
201
views
Find ASVs for Non-Microbial Data
Amplicon
ASV
PCR
BWA
VCF
updated 5 days ago by
andres.firrincieli
3.1k • written 6 days ago by
Saran
▴ 20
0
votes
0
replies
200
views
Installation paths not writeable, unable to update packages error in installing methimpute
r
RNA-seq
updated 6 days ago by
Ram
37k • written 15 days ago by
sam
• 0
1
vote
3
replies
199
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 38 minutes ago by
Wayne
★ 1.6k • written 4 days ago by
Aidand
• 0
0
votes
3
replies
197
views
Downloading 450k methylation data from GEO
minfi
450K
IDAT
Methylation
GEO
updated 6 days ago by
GenoMax
125k • written 6 days ago by
Edward E-B
• 0
1
vote
2
replies
197
views
How to install pandas
ml
python
offtopic
updated 6 days ago by
Ram
37k • written 7 days ago by
Sargun
• 0
0
votes
3
replies
197
views
Error while using rpy2
R
rpy2
Python
updated 5 days ago by
Wayne
★ 1.6k • written 7 days ago by
sidrah.maryam
▴ 40
2
votes
0
replies
196
views
Should one concatenate two haplotype genome assemblies into one assembly?
PacBio
genome-assembly
whole-genome-sequence
Hi-C
updated 3 days ago by
Ram
37k • written 12 months ago by
anikcropscience
▴ 150
0
votes
0
replies
193
views
Comparative genomic analysis for domestication related traits
genomics
updated 3 days ago by
Ram
37k • written 4 weeks ago by
shwetamgr1
▴ 10
0
votes
3
replies
192
views
Help interpreting FastQC report
fastQC
trimming
quality-control
updated 6 days ago by
GenoMax
125k • written 7 days ago by
sithlordashley
• 0
0
votes
2
replies
190
views
No variants found ( have problem in the handbook)
bcftools
handbook
variation_calling
igv
5 days ago by
quanyu
• 0
0
votes
0
replies
189
views
Unrooted consensus tree [Bio.Phylo]
consensus
phylo
biopython
2 days ago by
Jimpix
▴ 10
0
votes
0
replies
189
views
Issues Using DMRcate and rmSNPandCH
DMRcate
R
1 hour ago by
Indira
• 0
0
votes
0
replies
188
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs
ploidy
2 days ago by
optimistsso4co3
▴ 100
0
votes
1
reply
187
views
How to analysis genomes with orthologs?
ortholog
genome
annotation
updated 4 days ago by
GenoMax
125k • written 4 days ago by
沛煒
• 0
1
vote
1
reply
182
views
Visualize variants and percentage of variants from one sample of Amplicon Seq data?
Amplicon
PCR
RNAseq
GATK
BWA
updated 4 days ago by
cmdcolin
★ 2.8k • written 5 days ago by
Saran
▴ 20
0
votes
3
replies
182
views
blast engine error empty blast query vector
error
alignment
Blast
updated 5 days ago by
pbioinf
▴ 30 • written 5 days ago by
Sowmya Pulapet
▴ 10
0
votes
0
replies
181
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
3 days ago by
bioinfo
▴ 20
0
votes
0
replies
181
views
GSEA multiple group analysis
gsea
single-cell
2 days ago by
piotto
▴ 10
0
votes
0
replies
181
views
vcf2maf - generate 1 maf for 2 vcf files
maf
WES
vcf2maf
updated 6 days ago by
Ram
37k • written 9 days ago by
CH1374
▴ 10
3
votes
2
replies
178
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 4 days ago by
rpolicastro
11k • written 5 days ago by
janinubinu
• 0
1
vote
1
reply
172
views
bwa mem duration?
performance
mapping
bwa
updated 3 days ago by
ATpoint
68k • written 3 days ago by
lacb
▴ 30
0
votes
0
replies
174
views
SpliceAi same variant , different score
SpliceAi
updated 2 days ago by
Pierre Lindenbaum
152k • written 2 days ago by
vvasta
• 0
0
votes
0
replies
171
views
gistic- overlapp
CNV
GISTIC
TCGA
2 days ago by
Hanie
• 0
0
votes
2
replies
170
views
Where can I get the ICB datasets in this website?
data
r
ICB
updated 5 days ago by
GenoMax
125k • written 6 days ago by
JACKY
▴ 70
1
vote
1
reply
170
views
tools that align sequences in mouse and human
r
updated 5 days ago by
dthorbur
▴ 260 • written 5 days ago by
Chironex
▴ 40
0
votes
0
replies
169
views
Sequence Homology locator
Sequence
Homology
Genome
finder
2 days ago by
himalayan_yeti
• 0
0
votes
1
reply
169
views
Identifying whether a sequence is Novel or not
Novel-sequence
WGS
updated 3 days ago by
Ram
37k • written 14 days ago by
Mustafa
• 0
0
votes
0
replies
167
views
Combining samtools view command for selecting reads by their flag value
alignment
samtools
next-gen-sequencing
updated 6 days ago by
Ram
37k • written 9 weeks ago by
barzilayrom1
▴ 10
0
votes
0
replies
161
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
3 days ago by
anubratadas
▴ 20
0
votes
1
reply
159
views
How to choose --mind value for plink SNPs filtering
SNPs
mind
plink
filter
updated 20 hours ago by
Fabio Marroni
★ 2.9k • written 6 days ago by
anithanagaraj93
• 0
0
votes
1
reply
159
views
Compare population structure results
plots
circlize
dendextend
R
updated 6 days ago by
size_t
▴ 40 • written 7 days ago by
waqaskhokhar999
▴ 150
0
votes
0
replies
159
views
VNTR genotyping
NGS
VNTR
genotyping
3 days ago by
Genotepes
▴ 950
0
votes
1
reply
158
views
Remove duplicates in multifasta, where entries are paired
bash
python
updated 3 days ago by
dthorbur
▴ 260 • written 4 days ago by
SaltedPork
▴ 170
0
votes
0
replies
153
views
How to select reads that correspond to one or more specific flag values
alignment
samtools
next-gen-sequencing
updated 6 days ago by
Ram
37k • written 9 weeks ago by
barzilayrom1
▴ 10
0
votes
0
replies
152
views
scATAC merging of files
Signac
scATAC-seq
3 days ago by
bioinformatics.girl
• 0
0
votes
0
replies
152
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
3 days ago by
manaswiniparija3
▴ 10
0
votes
0
replies
151
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
3 days ago by
bioinfo
▴ 20
0
votes
2
replies
147
views
scATAC-seq workflow
Signac
scATAC-seq
20 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
145
views
Scanpy - highest expressed genes
normalization
Scanpy
scRNA
updated 3 days ago by
Ram
37k • written 8 days ago by
mt_pereira
• 0
0
votes
0
replies
144
views
How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression
miRNA
correlation
5 days ago by
Zahra
▴ 90
0
votes
0
replies
140
views
Bootstrap in PhyML
phyml
bootstrap
4 days ago by
Jimpix
▴ 10
0
votes
0
replies
138
views
Statistical test on two phylogenetically remote groups
phylogeny
ANOVA
1 day ago by
liorglic
★ 1.1k
0
votes
1
reply
138
views
f-index in treemix
treemix
introgression
f-index
1 day ago by
kk.mahsa
▴ 140
0
votes
0
replies
136
views
Anti-CRISPR and Cas protein interactions
crispr
anti-crispr
proteins
updated 5 days ago by
GenoMax
125k • written 5 days ago by
Moein
• 0
0
votes
0
replies
135
views
Application of the branch, site and branch-site models for detecting selection with codeml (PAML)
evolution
codeml
PAML
5 days ago by
Denis
▴ 260
0
votes
0
replies
135
views
Normalizing expression values
normalization
Scanpy
logCPM
scRNA
updated 3 days ago by
Ram
37k • written 8 days ago by
mt_pereira
• 0
0
votes
0
replies
134
views
issues with amber_minimize.py failing to use CUDA within alphafold
linux
CUDA
amber
alphafold
5 days ago by
charlieclark1ee
▴ 10
0
votes
0
replies
131
views
Enrichment map in python/ Pathway network by using python
interaction.
enrichment
network
pathway
analysis
4 days ago by
sonsunjirachote
• 0
0
votes
0
replies
127
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
3 days ago by
a.bibek52
• 0
0
votes
0
replies
126
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
3 days ago by
a.bibek52
• 0
194 results • Page
3 of 4
Recent Votes
REDItools VS GATK haplotype caller
Comment: fastqc: Per base sequence content
Comment: fastqc: Per base sequence content
Comment: Size of two scRNA-Seq conditions
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
What type of database does gnomAD use?
What type of database does gnomAD use?
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Comment: SNP calling
by
dthorbur
▴ 260
No idea about the second error, but the first error seems odd to me. What version of GATK are you using? I thought recent versions only emi…
Comment: Size of two scRNA-Seq conditions
by
Chris
▴ 60
Thank you so much for your answer! Here is the structure of 2 matrix objects of two conditions. Condition 1 has 19760 cells meanwhile condi…
Answer: Mapping with bbmap.sh
by
Mensur Dlakic
★ 22k
Definitely not normal. It doesn't seem that BBmap is taking any reads in. That's why your `num reads` and `num bases` are all zeros, which…
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Mensur Dlakic
★ 22k
I have no idea what cutoff is in this context, nor what you mean by `original` values. I don't know how you got those values for means. I …
Comment: Protein protein interactions
by
Mensur Dlakic
★ 22k
This is not a trivial calculation nor a simple sequence comparison like with BLAST, so it may take a while. Besides, there could be hundred…
Comment: snakemake Unexpected keyword bam in rule definition
by
Wayne
★ 1.6k
Any chance it is an indentation issue that isn't caused by what you aren't sharing here? See [here](https://groups.google.com/g/snakemake/c…
Comment: Size of two scRNA-Seq conditions
by
rpolicastro
11k
More important would be the cell QC stats (such as reads per cell and number of unique features detected per cell), the number of cells per…
Answer: What type of database does gnomAD use?
by
Jeremy Leipzig
21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
by
Basti
★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box
by
Ram
37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function
by
jv
▴ 790
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
• 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans
by
GenoMax
125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
by
jv
▴ 790
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content
by
jv
▴ 790
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
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