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1,000 results • Page
4 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
349
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
6 days ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 6 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
2
votes
7
replies
794
views
Removing duplicates
duplicates
ONT
minimap2
updated 4 days ago by
joe
▴ 510 • written 6 days ago by
quentinperriere
• 0
0
votes
1
reply
191
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 6 days ago by
DKA
▴ 40 • written 6 days ago by
james.melhorn
• 0
3
votes
4
replies
412
views
biomaRt error for different R version
biomaRt
R
updated 5 days ago by
GenoMax
141k • written 6 days ago by
manaswwm
▴ 490
0
votes
1
reply
177
views
Freyja plot error
Freyja
updated 6 days ago by
Ram
43k • written 6 days ago by
Adyasha
• 0
1
vote
2
replies
191
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
6 days ago by
hagl
▴ 10
0
votes
0
replies
152
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
6 days ago by
chemokine-1
▴ 10
0
votes
4
replies
486
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
5 days ago by
feather-W
• 0
0
votes
0
replies
220
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 6 days ago by
Michael
54k • written 6 days ago by
jonrkarr
▴ 100
0
votes
2
replies
209
views
Bedmethyl file format
bedmethyl
methylation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
njornet
▴ 20
0
votes
0
replies
164
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
6 days ago by
Ali
• 0
2
votes
4
replies
303
views
SnpEff annotates coding duplication as intronic?
snpeff
6 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
235
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
6 days ago by
mropri
▴ 150
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 6 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
593
views
Piping samtools to R
R
NGS
bash
samtools
6 days ago by
joe
▴ 510
2
votes
2
replies
234
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 6 days ago by
bk11
★ 2.3k • written 6 days ago by
bgbs
• 0
3
votes
7
replies
437
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
6 days ago by
ntsopoul
▴ 60
0
votes
0
replies
138
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
6 days ago by
shasabhi1
• 0
0
votes
0
replies
129
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
6 days ago by
Nishat
• 0
3
votes
3
replies
403
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
6 days ago by
ayushm64
• 0
0
votes
0
replies
150
views
what exactly is a k-mer table (remora)?
remora
basecall
6 days ago by
anne
• 0
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 6 days ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
393
views
Rename multiple fastq.gz files
fastq
next-gen
updated 6 days ago by
shenwei356
8.4k • written 7 days ago by
Jérémie
• 0
1
vote
1
reply
170
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 7 days ago by
dsull
★ 5.8k • written 7 days ago by
niruf
• 0
0
votes
0
replies
178
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
1 day ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
269
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 7 days ago by
GenoMax
141k • written 7 days ago by
lorena9132
• 0
0
votes
0
replies
168
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
David Langenberger
11k
0
votes
0
replies
136
views
GWAS Phenotypes
GWAS
7 days ago by
solomoncharles77
▴ 90
4
votes
2
replies
270
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 7 days ago by
Ram
43k • written 7 days ago by
Adi
▴ 10
0
votes
2
replies
301
views
GSEA analysis in R
GSEA
R
Arabidopsis
5 days ago by
Sudip
• 0
1
vote
2
replies
249
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 7 days ago by
Joe
21k • written 8 days ago by
ferdinand
▴ 10
0
votes
2
replies
361
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
6 days ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
379
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 7 days ago by
Ram
43k • written 7 days ago by
Spring
• 0
0
votes
0
replies
119
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
7 days ago by
QX
• 0
5
votes
4
replies
295
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
7 days ago by
Spring
• 0
2
votes
5
replies
418
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
6 days ago by
Bikram Kumar
• 0
1
vote
1
reply
286
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 7 days ago by
andres.firrincieli
3.6k • written 11 days ago by
Milly
• 0
0
votes
1
reply
209
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 7 days ago by
ATpoint
81k • written 7 days ago by
Ravita
• 0
0
votes
2
replies
221
views
Getting marker genes for cell types
clustering
marker-genes
umap
7 days ago by
orzrzlyo
▴ 20
0
votes
1
reply
215
views
gene body coverage with RSeqQC
rna-seq
qc
updated 7 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
wiscoyogi
▴ 40
0
votes
2
replies
249
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 7 days ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
1
reply
188
views
Using adonis to include a random effect
mixed-model
adonis
updated 7 days ago by
LChart
3.9k • written 7 days ago by
leranwangcs
▴ 120
1
vote
3
replies
426
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 7 days ago by
LChart
3.9k • written 8 days ago by
leranwangcs
▴ 120
1
vote
2
replies
258
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
6 days ago by
bioinfo
▴ 150
0
votes
1
reply
184
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 7 days ago by
bk11
★ 2.3k • written 7 days ago by
sinhas
• 0
1
vote
5
replies
353
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
7 days ago by
shpak.max
▴ 50
0
votes
1
reply
199
views
merging Seurat objects after SCT
Seurat
SCT
updated 7 days ago by
Ram
43k • written 7 days ago by
michelle.swarovski
• 0
0
votes
1
reply
191
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 8 days ago by
GenoMax
141k • written 8 days ago by
haiying.kong
▴ 360
0
votes
2
replies
256
views
RNAseq 1 control 2 different treatment
RNA-seq
7 days ago by
matteo.levorato
• 0
1,000 results • Page
4 of 20
Recent Votes
Trimming sequences based on NCBI contamination screen report
warning[vg::giraffe]: Cannot cluster reads with a fragment distance smaller than read distance
Answer: Redirection of Duplicate PMIDs
Answer: How to convert plink files to Hapmap Format
Answer: How to convert plink files to Hapmap Format
Comment: Redirection of Duplicate PMIDs
Comment: Failed kmer content
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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this with a couple of random grants …
Answer: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Hi Dominick, One thing I am not sure of is, how is it that you got the other PMID in the first place? The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
Comment: Subset Seurat object from Xenium spatial data
by
bk11
★ 2.3k
For subsetting a sample, you can do something like this- Idents(seuratObj) <- "orig.ident" subj1 <- c("subject_1") subj1_seur…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Ok! I have a recommendation. I'll submit it as an answer, pending your feedback. vincent
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
In modeller we need to use templates as well.so 63% is acceptable
Comment: DYH17 Structure Prediction
by
Ram
43k
Mensur said > The latter option assumes you know how to use Modeller Do you know how to use Modeller? I vaguely recall there being a mini…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
OP is working with long reads so the chances of reads aligning to unlocalized scaffolds are relatively small. Doing some testing may be suf…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
ATpoint
81k
I personally think that comparing the same peak between conditions is meaningful and comparing peaks within the same sample is not.
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
ATpoint
81k
These regions are present in the genome and removing them might incorrectly redirect alignments to known genes. I don't see why you would r…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
Comment: Using vg gamsort with naive sorting algorithm
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
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