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85 results • Page
2 of 2
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Views
Votes
Replies
0
votes
0
replies
133
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
6 days ago by
Mamatha Y S
• 0
0
votes
0
replies
138
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
6 days ago by
rthapa
▴ 90
0
votes
0
replies
139
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 5 days ago by
Ram
43k • written 5 days ago by
sainavyav22
• 0
0
votes
0
replies
127
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
Atul K.
• 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
4 days ago by
Biostars2200
• 0
0
votes
0
replies
74
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
4 days ago by
sativus
▴ 20
0
votes
0
replies
91
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
4 days ago by
Enrique
• 0
0
votes
0
replies
73
views
Imputation advice
imputation
4 days ago by
kl
▴ 10
0
votes
0
replies
82
views
Annotating single cell data automatically
cell
annotation
single
4 days ago by
Gerard
• 0
0
votes
0
replies
83
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
4 days ago by
feather-W
• 0
0
votes
0
replies
86
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
4 days ago by
manaswwm
▴ 490
0
votes
0
replies
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
4 days ago by
Javier
• 0
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 4 days ago by
Ram
43k • written 4 days ago by
sansan_96
▴ 80
0
votes
0
replies
197
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 4 days ago by
Ram
43k • written 4 days ago by
Oak
▴ 10
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 4 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
0
replies
108
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 4 days ago by
Ram
43k • written 4 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
76
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 days ago by
alifafiq1
• 0
0
votes
0
replies
97
views
Merging replicates from Encode project
CHIP-seq
encode
3 days ago by
Nurken
• 0
0
votes
0
replies
89
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 3 days ago by
Ram
43k • written 3 days ago by
SHREYA
• 0
0
votes
0
replies
95
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 3 days ago by
Ram
43k • written 4 days ago by
Amélie
• 0
0
votes
0
replies
96
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
3 days ago by
ohtang7
▴ 40
0
votes
0
replies
86
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 3 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
0
replies
106
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
3 days ago by
Kash
▴ 110
0
votes
0
replies
133
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
0
votes
0
replies
267
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
2 days ago by
pramach1
▴ 40
0
votes
0
replies
131
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 2 days ago by
Ram
43k • written 2 days ago by
glaciya2018
• 0
0
votes
0
replies
114
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 2 days ago by
Ram
43k • written 2 days ago by
newuser2024
• 0
0
votes
0
replies
95
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 2 days ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
0
replies
119
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 day ago by
4fzcgueyp5
• 0
0
votes
0
replies
97
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
0
votes
0
replies
84
views
how to read graph_test output of monocle 3
monocle3
1 day ago by
synat.keam
▴ 100
1
vote
0
replies
99
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
1 day ago by
rohitsatyam102
▴ 850
0
votes
0
replies
79
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 day ago by
Emily
▴ 10
0
votes
0
replies
90
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
1 day ago by
avocado123
• 0
0
votes
0
replies
77
views
Designing single-stable RNA molecules
structure
RNA
1 day ago by
Edna
• 0
85 results • Page
2 of 2
Recent Votes
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
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Recent Replies
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
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35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
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Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
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19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
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If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
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jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
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I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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