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116,627 results • Page
3 of 2333
Sort: Rank
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Votes
Replies
0
votes
3
replies
216
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 4 days ago by
mchour
• 0 • written 4 days ago by
rhossen
• 0
1
vote
1
reply
161
views
WGCNA preservation analysis
WGCNA
preservation
updated 4 days ago by
Michael
54k • written 4 days ago by
michael.flower.14
▴ 180
1
vote
3
replies
263
views
some error in building kraken2 database
metagenome
kraken2
3 days ago by
Art1ess
• 0
0
votes
1
reply
139
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 4 days ago by
bk11
★ 2.4k • written 4 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
134
views
Plots for DNA methylation data
plots
DNA
methylation
updated 4 days ago by
GenoMax
141k • written 4 days ago by
sarahawan92
▴ 10
0
votes
3
replies
492
views
python file for coding potential calculator
cpc2.py
updated 4 days ago by
atharvakarkare14
▴ 10 • written 8 days ago by
Ashok
• 0
1
vote
1
reply
170
views
Failed kmer content
kmer
illumina
ngs
updated 4 days ago by
Ram
43k • written 4 days ago by
Kasturi
• 0
0
votes
0
replies
162
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
4 days ago by
yxwucq
• 0
0
votes
0
replies
87
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 4 days ago by
SSSJec
• 0
0
votes
6
replies
317
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
3 days ago by
Sd
• 0
0
votes
2
replies
180
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
4 days ago by
sainavyav22
• 0
0
votes
1
reply
146
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 4 days ago by
Ram
43k • written 4 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
328
views
Error in cnetplot enrichplot package
R
updated 4 days ago by
Ram
43k • written 4 days ago by
Farhad
• 0
3
votes
9
replies
442
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 3 days ago by
Istvan Albert
100k • written 4 days ago by
Κοσμάς
• 0
0
votes
0
replies
110
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
3
votes
3
replies
197
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
c_u
▴ 520
0
votes
0
replies
93
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
96
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 4 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
2
votes
3
replies
204
views
from row count to tpm
tpm
row-count
normalization
4 days ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
281
views
Downsampling fastq file
downsample
fastq
updated 4 days ago by
Ram
43k • written 5 days ago by
marco.barr
▴ 80
2
votes
3
replies
323
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.8k • written 17 days ago by
javanokendo
▴ 60
0
votes
1
reply
136
views
tbtool
tbtool
updated 4 days ago by
Ram
43k • written 5 days ago by
Raman
• 0
0
votes
7
replies
314
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
GenoMax
141k • written 5 days ago by
Patadu94
• 0
3
votes
3
replies
226
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Mariana
▴ 10
0
votes
1
reply
128
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 5 days ago by
ATpoint
82k • written 5 days ago by
enanoide
• 0
0
votes
0
replies
88
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
5 days ago by
manaswwm
▴ 490
3
votes
3
replies
719
views
KissDE and batch effect
kissDE
kissplice
5 days ago by
david.b.rombaut
▴ 10
0
votes
0
replies
78
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
4 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
2 days ago by
Kevin Blighe
87k
0
votes
0
replies
84
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
5 days ago by
feather-W
• 0
2
votes
4
replies
275
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
3 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
84
views
Annotating single cell data automatically
cell
annotation
single
5 days ago by
Gerard
• 0
0
votes
0
replies
83
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
128
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
5 days ago by
Ben_Ensembl
★ 2.4k
2
votes
4
replies
312
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
3 days ago by
HyperEvo
• 0
0
votes
1
reply
153
views
RNA-seq bacteria contamination
RNA-seq
updated 5 days ago by
GenoMax
141k • written 5 days ago by
sh
• 0
0
votes
2
replies
194
views
Result of running of p3_in.pl
primer3
updated 5 days ago by
GenoMax
141k • written 5 days ago by
nasri
• 0
0
votes
1
reply
135
views
FAM FILE
file
Fam
5 days ago by
Eleonora
• 0
0
votes
0
replies
74
views
Imputation advice
imputation
5 days ago by
kl
▴ 10
3
votes
5
replies
271
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 5 days ago by
GenoMax
141k • written 5 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
92
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
5 days ago by
Enrique
• 0
3
votes
5
replies
551
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
5 days ago by
n_navy
• 0
0
votes
0
replies
75
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
5 days ago by
sativus
▴ 20
6
votes
3
replies
184
views
Interpretting IGV output
IGV
updated 5 days ago by
Carlo Yague
8.7k • written 5 days ago by
analyst
▴ 30
0
votes
1
reply
177
views
homology modelling using swiss model
homology-modeling
swiss-model
updated 5 days ago by
colindaven
6.4k • written 6 days ago by
Ayush
• 0
0
votes
0
replies
81
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
5 days ago by
Biostars2200
• 0
1
vote
5
replies
338
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
4 days ago by
anasjamshed
▴ 120
0
votes
0
replies
130
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 5 days ago by
Carlo Yague
8.7k • written 5 days ago by
Atul K.
• 0
116,627 results • Page
3 of 2333
Recent Votes
Calculate Allele balance by sample
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
Answer: Heatmap and rna-seq
Answer: How to use limma to find differentially expressed genes in response to a continu
A: Blast Settings For Short Sequences
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rohitsatyam102
▴ 850
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candron
▴ 10
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35k
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Recent Replies
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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
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…
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