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510 results • Page
2 of 11
Sort: Rank
Rank
Views
Votes
Replies
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
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
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 4 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
273
views
Downsampling fastq file
downsample
fastq
updated 4 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 80
0
votes
1
reply
134
views
tbtool
tbtool
updated 4 days ago by
Ram
43k • written 4 days ago by
Raman
• 0
0
votes
7
replies
304
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 13 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
1
reply
127
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 4 days ago by
ATpoint
82k • written 4 days ago by
enanoide
• 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
78
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 days ago by
alifafiq1
• 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
2
votes
4
replies
271
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
2 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
83
views
Annotating single cell data automatically
cell
annotation
single
4 days ago by
Gerard
• 0
0
votes
1
reply
151
views
RNA-seq bacteria contamination
RNA-seq
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sh
• 0
0
votes
0
replies
73
views
Imputation advice
imputation
4 days ago by
kl
▴ 10
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
4 days ago by
Enrique
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
4 days ago by
sativus
▴ 20
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
129
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 5 days ago by
Atul K.
• 0
2
votes
5
replies
452
views
Marking duplicates using UMIs
Deduplication
UMI
updated 4 days ago by
i.sudbery
19k • written 6 days ago by
Lipika
• 0
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 6 days ago by
sainavyav22
• 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
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
2
replies
262
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
542
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
6 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
213
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
6 days ago by
abhishekghadge
• 0
2
votes
5
replies
687
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 6 days ago by
Jesse
▴ 740 • written 7 days ago by
Ann
★ 2.4k
0
votes
0
replies
187
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 7 days ago by
Ram
43k • written 7 days ago by
mja
• 0
0
votes
0
replies
189
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
7 days ago by
Nitin
• 0
0
votes
0
replies
189
views
absolute path for symbolic links in Snakefile
Snakemake
updated 7 days ago by
Ram
43k • written 7 days ago by
yifangt86
▴ 60
0
votes
0
replies
181
views
Chemical structure validation
structure
cap
validation
metabolite
7 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
261
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 7 days ago by
GenoMax
141k • written 7 days ago by
bioyas
▴ 10
0
votes
0
replies
205
views
Copy number variation plot
Copy-number-variation
genomics
updated 7 days ago by
Ram
43k • written 7 days ago by
Emmi
• 0
0
votes
0
replies
180
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
7 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
284
views
Could you please assist in identifying this cluster?
single-cell
updated 7 days ago by
Ram
43k • written 7 days ago by
Kazo
• 0
0
votes
0
replies
198
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 7 days ago by
Ram
43k • written 7 days ago by
Dinmukhamed
• 0
0
votes
0
replies
196
views
miRDeep2: How to get the read counts
mirdeep2
7 days ago by
Atul K.
• 0
0
votes
0
replies
201
views
Lncipedia GTF file error
Proteomics
updated 7 days ago by
Ram
43k • written 7 days ago by
atharvakarkare14
▴ 10
3
votes
3
replies
471
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 8 days ago by
joe
▴ 510
0
votes
2
replies
538
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
8 days ago by
航太郎
• 0
0
votes
0
replies
214
views
create genewise sync file in popoolation
popoolation
updated 8 days ago by
GenoMax
141k • written 8 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
374
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
8 days ago by
Ashok
• 0
0
votes
2
replies
411
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
7 days ago by
Ashok
• 0
0
votes
0
replies
213
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 8 days ago by
Ram
43k • written 8 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
423
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
7 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
203
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
179
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
8 days ago by
enferdeflame
• 0
1
vote
1
reply
417
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
0
votes
1
reply
401
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 8 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
159
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 8 days ago by
Ram
43k • written 8 days ago by
bioinfo223
▴ 10
0
votes
0
replies
176
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
8 days ago by
P.
• 0
510 results • Page
2 of 11
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Recent Awards •
All
Scholar
to
Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Commentator
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GenoMax
141k
Popular Question
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rheab1230
▴ 140
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BioinfGuru
★ 1.7k
Scholar
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bk11
★ 2.4k
Popular Question
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vinayjrao
▴ 250
Recent Replies
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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
by
Alex Reynolds
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…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
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
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
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
by
BioinfGuru
★ 1.7k
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
by
i.sudbery
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…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
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…
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