Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
3
votes
2
replies
273
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
4 days ago by
kristiewyleung
• 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
0
replies
130
views
News:
upcoming online statistical courses
Statistics
R
Data-Analysis
updated 5 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
4
replies
524
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 6 days ago by
ATpoint
82k • written 7 days ago by
rheab1230
▴ 140
0
votes
2
replies
261
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
7
votes
6
replies
470
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
5 days ago by
analyst
▴ 30
1
vote
1
reply
257
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 6 days ago by
Gordon Smyth
★ 7.0k • written 7 days ago by
Bioinformatician
• 0
1
vote
0
replies
540
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
1
vote
1
reply
299
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 6 days ago by
Ram
43k • written 7 days ago by
Nina
• 0
2
votes
5
replies
521
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 6 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
Giorgio
• 0
2
votes
1
reply
287
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 7 days ago by
GenoMax
141k • written 7 days ago by
rebecca.calvo
• 0
0
votes
0
replies
212
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
685
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
1
vote
5
replies
561
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 7 days ago by
GenoMax
141k • written 7 days ago by
Luka
• 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
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 6 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
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
1
vote
5
replies
701
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 7 days ago by
BioinfGuru
★ 1.7k • written 8 days ago by
rrehimi
• 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
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 7 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 6 days ago by
ATpoint
82k • written 7 days ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
412
views
Plink merge errors.
cygwin64
bed
PLINK
7 days ago by
Dinmukhamed
• 0
0
votes
0
replies
197
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
3
votes
4
replies
657
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
4 days ago by
rahu
• 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
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 7 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
471
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
0
votes
2
replies
537
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
8 days ago by
航太郎
• 0
11
votes
12
replies
951
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 8 days ago by
Ram
43k • written 8 days ago by
iamsmor
• 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
373
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
7 days ago by
Ashok
• 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
7 days ago by
Ashok
• 0
0
votes
0
replies
212
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
1
vote
1
reply
369
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
8 days ago by
otieno43
▴ 30
0
votes
2
replies
422
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
202
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
4 days ago by
Javier
• 0
1
vote
4
replies
685
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 8 days ago by
Ram
43k • written 3 months ago by
turcoa1
• 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 5 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
0
votes
0
replies
189
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 8 days ago by
Ram
43k • written 8 days ago by
carlopecoraro2
★ 2.5k
1,000 results • Page
4 of 20
Recent Votes
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
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
Recent Locations •
All
United States,
2 minutes ago
United States,
6 minutes ago
Russia,
10 minutes ago
Cambridge, MA,
20 minutes ago
United States,
22 minutes ago
India,
24 minutes ago
USA,
32 minutes ago
Recent Awards •
All
Scholar
to
Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Commentator
to
GenoMax
141k
Popular Question
to
rheab1230
▴ 140
Popular Question
to
BioinfGuru
★ 1.7k
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
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
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…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
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
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Traffic: 1800 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6