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397 results • Page
5 of 8
Sort: Votes
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Views
Votes
Replies
0
votes
5
replies
269
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 7 days ago by
Joe
21k • written 7 days ago by
Lemonhope
• 0
0
votes
4
replies
296
views
Correlation Analysis
statistics
methylation
NGS
expression
4 days ago by
Researcher
▴ 30
0
votes
0
replies
174
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
20 days ago by
Aspire
▴ 330
0
votes
0
replies
109
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
13 days ago by
James
▴ 10
0
votes
0
replies
167
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
21 days ago by
salias
• 0
0
votes
1
reply
54
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 2 hours ago by
yura.grabovska
▴ 70 • written 2 hours ago by
ev97
▴ 20
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
2 days ago by
lagartija
▴ 160
0
votes
1
reply
115
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
15 hours ago by
sansan_96
▴ 90
0
votes
0
replies
107
views
Normalizing AMR gene count data
abundance
RGI
updated 9 days ago by
Ram
43k • written 9 days ago by
arshad1292
▴ 100
0
votes
0
replies
170
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
19 days ago by
turcoa1
• 0
0
votes
0
replies
39
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
3 hours ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
105
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
23 days ago by
manaswwm
▴ 510
0
votes
0
replies
329
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
12 days ago by
NorbertK
▴ 10
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 22 days ago by
Ram
43k • written 22 days ago by
SSSJec
• 0
0
votes
0
replies
207
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
26 days ago by
Nitin
• 0
0
votes
2
replies
282
views
How are score_weights calculated in this code?
single-cell
4 days ago by
carolofharvest
▴ 40
0
votes
0
replies
199
views
Chemical structure validation
structure
cap
validation
metabolite
26 days ago by
Rodolfo Adrián
• 0
0
votes
2
replies
223
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 4 days ago by
Ram
43k • written 6 days ago by
sainavyav22
• 0
0
votes
0
replies
124
views
How to implement an IGV to streamlit app?
python
streamlit
igv
9 days ago by
avigail.shnaider
• 0
0
votes
3
replies
313
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 15 days ago by
GenoMax
142k • written 15 days ago by
kim
• 0
0
votes
0
replies
89
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
0
replies
224
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
19 days ago by
HarperReed
• 0
0
votes
0
replies
157
views
supervised admixture
supervised
admixture
5 days ago by
RT
▴ 10
0
votes
0
replies
157
views
Filter low express genes in microarray data
microarray
18 days ago by
Chris
▴ 280
0
votes
1
reply
155
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 27 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
1
reply
217
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 5 days ago by
curious
▴ 750 • written 5 days ago by
SeoGyun
• 0
0
votes
0
replies
186
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
6 days ago by
Matvii Mykhailichenko
• 0
0
votes
4
replies
411
views
Highest variable features in single cell data
single-cell
8 days ago by
carolofharvest
▴ 40
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 28 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
0
votes
3
replies
331
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
231
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 27 days ago by
Ram
43k • written 27 days ago by
samuelkalandarov2002
▴ 10
0
votes
3
replies
101
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
8 hours ago by
Esraa
• 0
0
votes
0
replies
105
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R
RUV
methylation
missmethyl
batch-effect
updated 28 days ago by
Ram
43k • written 6.0 years ago by
RC
▴ 20
0
votes
0
replies
109
views
Cellphonedb results
cpdb
visulization
cellphonedb
8 days ago by
piotto
▴ 20
0
votes
0
replies
157
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
14 days ago by
O.rka
▴ 720
0
votes
2
replies
308
views
Annovar using R package
Annovar
gnomAD
R
19 days ago by
DKA
▴ 40
0
votes
2
replies
224
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
2 days ago by
analyst
▴ 50
0
votes
0
replies
227
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
23 days ago by
Javier
• 0
0
votes
0
replies
1.8k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect
RNA-Seq
Differential-Expression
updated 28 days ago by
Ram
43k • written 7.2 years ago by
vakul.mohanty
▴ 270
0
votes
1
reply
558
views
HOMER on AWS
HOMER
updated 12 days ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 26 days ago by
GenoMax
142k • written 27 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
1
reply
168
views
tbtool
tbtool
updated 23 days ago by
Ram
43k • written 23 days ago by
Raman
• 0
0
votes
0
replies
208
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 26 days ago by
Ram
43k • written 26 days ago by
mja
• 0
0
votes
0
replies
95
views
Imputation advice
imputation
23 days ago by
kl
▴ 10
0
votes
3
replies
355
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 16 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
0
votes
2
replies
268
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 5 days ago by
GenoMax
142k • written 11 days ago by
Ximena
• 0
0
votes
0
replies
196
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
27 days ago by
P.
• 0
0
votes
0
replies
1.9k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq
gene-expression-matrix
correlation
R
updated 28 days ago by
Ram
43k • written 6.3 years ago by
aiswaryabioinfo
▴ 30
397 results • Page
5 of 8
Recent Votes
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
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Recent Replies
Comment: Doubt about the process of annotation, detection, identification and classificat
by
MarcosCosta
• 0
Thank you very much, you've helped me a lot
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
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