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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
407
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
7 days ago by
renan.igor
• 0
0
votes
0
replies
179
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
9 days ago by
synat.keam
▴ 100
0
votes
1
reply
268
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 9 days ago by
GenoMax
141k • written 9 days ago by
ycts
• 0
0
votes
4
replies
580
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
8 days ago by
Kai Xin
• 0
1
vote
1
reply
226
views
Retrieve a % coverage for each transcript
RNA-seq
updated 9 days ago by
Ram
43k • written 9 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
372
views
How can I solve this error?
metal
9 days ago by
22211020193
• 0
0
votes
0
replies
166
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 9 days ago by
GenoMax
141k • written 9 days ago by
srimmer
• 0
1
vote
2
replies
276
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 9 days ago by
Ram
43k • written 9 days ago by
aniigodwinn
• 0
0
votes
0
replies
354
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
10 days ago by
Ronin
• 0
2
votes
7
replies
822
views
Removing duplicates
duplicates
ONT
minimap2
updated 8 days ago by
joe
▴ 510 • written 10 days ago by
quentinperriere
• 0
0
votes
1
reply
197
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 10 days ago by
DKA
▴ 40 • written 10 days ago by
james.melhorn
• 0
0
votes
1
reply
188
views
Freyja plot error
Freyja
updated 9 days ago by
Ram
43k • written 10 days ago by
Adyasha
• 0
0
votes
0
replies
156
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
10 days ago by
chemokine-1
▴ 10
0
votes
4
replies
505
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
9 days ago by
feather-W
• 0
0
votes
2
replies
224
views
Bedmethyl file format
bedmethyl
methylation
updated 10 days ago by
GenoMax
141k • written 10 days ago by
njornet
▴ 20
0
votes
0
replies
168
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
10 days ago by
Ali
• 0
2
votes
4
replies
320
views
SnpEff annotates coding duplication as intronic?
snpeff
10 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
252
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
10 days ago by
mropri
▴ 150
0
votes
0
replies
143
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
10 days ago by
shasabhi1
• 0
0
votes
0
replies
134
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
10 days ago by
Nishat
• 0
0
votes
0
replies
161
views
what exactly is a k-mer table (remora)?
remora
basecall
10 days ago by
anne
• 0
1
vote
1
reply
180
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 10 days ago by
dsull
★ 5.8k • written 10 days ago by
niruf
• 0
0
votes
0
replies
143
views
GWAS Phenotypes
GWAS
11 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
318
views
GSEA analysis in R
GSEA
R
Arabidopsis
9 days ago by
Sudip
• 0
0
votes
0
replies
123
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
11 days ago by
QX
• 0
2
votes
5
replies
454
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
10 days ago by
Bikram Kumar
• 0
0
votes
2
replies
259
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 10 days ago by
Ram
43k • written 11 days ago by
David
• 0
1
vote
2
replies
270
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
10 days ago by
bioinfo
▴ 150
0
votes
1
reply
194
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 11 days ago by
bk11
★ 2.4k • written 11 days ago by
sinhas
• 0
0
votes
1
reply
208
views
merging Seurat objects after SCT
Seurat
SCT
updated 11 days ago by
Ram
43k • written 11 days ago by
michelle.swarovski
• 0
0
votes
1
reply
206
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 11 days ago by
GenoMax
141k • written 11 days ago by
haiying.kong
▴ 360
0
votes
2
replies
264
views
RNAseq 1 control 2 different treatment
RNA-seq
11 days ago by
matteo.levorato
• 0
1
vote
0
replies
143
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 11 days ago by
Ram
43k • written 11 days ago by
Oscar
▴ 10
0
votes
0
replies
156
views
How should I make kallisto indexes?
kallisto
updated 11 days ago by
GenoMax
141k • written 11 days ago by
bioinfo
▴ 150
2
votes
0
replies
206
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
12 days ago by
Alexander
▴ 220
1
vote
1
reply
181
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 12 days ago by
GenoMax
141k • written 12 days ago by
eesiribloom
▴ 80
0
votes
0
replies
137
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
12 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
142
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
12 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
151
views
FreeBayes detection capacity
reads
freebayes
long
12 days ago by
quentinperriere
• 0
0
votes
2
replies
249
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
10 days ago by
DKA
▴ 40
0
votes
0
replies
162
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
12 days ago by
Hien
• 0
0
votes
2
replies
293
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
10 days ago by
Koketso
• 0
0
votes
0
replies
192
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 12 days ago by
Ram
43k • written 13 days ago by
menyawino
• 0
1
vote
3
replies
352
views
Ensembl gene id conversion
biomart
ensembl
updated 11 days ago by
ATpoint
82k • written 13 days ago by
naveedhasan2000
• 0
1
vote
2
replies
319
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 11 days ago by
Istvan Albert
100k • written 13 days ago by
Jiang
• 0
0
votes
0
replies
192
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
14 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
317
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
13 days ago by
O.rka
▴ 710
0
votes
6
replies
552
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
11 days ago by
Dunois
★ 2.5k
4
votes
7
replies
556
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 13 days ago by
Ram
43k • written 14 days ago by
AHerik
▴ 20
0
votes
0
replies
187
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 14 days ago by
GenoMax
141k • written 14 days ago by
zec018
• 0
1,000 results • Page
3 of 20
Recent Votes
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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A: Blast Settings For Short Sequences
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Popular Question
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rohitsatyam102
▴ 850
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram
Comment: ScRNA data question
by
starswillfade
▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Guille
• 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
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
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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…
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by
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★ 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.
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