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119,074 results • Page
1 of 2382
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Why are the SINEs annotated as zero when using RepeatModeler + RepeatMasker?
SINEs
Repeatmodeler
RepeatMasker
just now by
15586642488
• 0
1
vote
1
reply
47
views
Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
Bioinformatics
RNAseq
Normalization
updated 31 minutes ago by
ATpoint
85k • written 4 hours ago by
wdasda122
▴ 10
0
votes
0
replies
20
views
Facing problems in analysis of bisulfite sequencing data
sequencing
Bisulfite
updated 37 minutes ago by
GenoMax
146k • written 1 hour ago by
SHREYA
• 0
0
votes
1
reply
71
views
Can anyone share with me the R code for GSEA analysis?
R
code
GSEA
updated 3 hours ago by
GenoMax
146k • written 5 hours ago by
nuorain
▴ 20
819
votes
169
replies
156k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 22 days ago by
Biostar
3.0k • written 7.8 years ago by
Istvan Albert
101k
0
votes
2
replies
137
views
extracting reads from FASTA/FASTQ file
RNA-seq
RNA
updated 6 hours ago by
GenoMax
146k • written 14 hours ago by
bleven
• 0
0
votes
2
replies
110
views
Different annotations for different isoforms from the same gene
metatranscriptomics
Trinity
RNA-seq
Isoform
6 hours ago by
Chikae
• 0
0
votes
0
replies
62
views
Forum:
epitope-TCR binding prediction, vaccine design
vaccine
epitope-TCR
binding
10 hours ago by
Dara
• 0
0
votes
0
replies
59
views
Forum:
layoffs in biotech
layoff
biotech
10 hours ago by
Dara
• 0
1
vote
1
reply
95
views
How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effects?
bulkRNAseq
lme4
updated 30 minutes ago by
ATpoint
85k • written 11 hours ago by
bioyas
▴ 20
0
votes
0
replies
61
views
Snakemake - pipeline shut down without error
snakemake
12 hours ago by
bhumm
▴ 170
0
votes
1
reply
82
views
DeSeq2 filter transcripts
DeSeq2
RNA-seq
RNA
updated 12 hours ago by
seidel
11k • written 13 hours ago by
bleven
• 0
0
votes
0
replies
50
views
Setting up a case control with 18 VCFs in plink?
case-control
plink
WGS
13 hours ago by
atopasn1
• 0
0
votes
1
reply
86
views
Aligning to transcriptome with STAR generates error in Salmon sequence length
STAR
Salmon
RNAseq
updated 6 hours ago by
Dunois
★ 2.6k • written 14 hours ago by
Lena
• 0
0
votes
1
reply
86
views
Gnomad result tables column meaning.
Gnomad
annotation
updated 14 hours ago by
Pierre Lindenbaum
164k • written 16 hours ago by
ijarne
▴ 10
1
vote
2
replies
126
views
DESeq2: adjusted p-values become NA when sub-setting samples
R
DEG
RNA-seq
DESeq2
updated 15 hours ago by
GenoMax
146k • written 16 hours ago by
txema.heredia
▴ 190
0
votes
1
reply
90
views
Trouble with Biopython residue depth
Proteins
Depth
Biopython
Residue
updated 14 hours ago by
Wayne
★ 2.0k • written 17 hours ago by
Anand KR
• 0
0
votes
2
replies
115
views
all genes have negative logFC edgeR
edgeR
updated 5 hours ago by
rfran010
★ 1.3k • written 18 hours ago by
xiaoyongli407
• 0
0
votes
1
reply
112
views
Split vcf file to fit tbi requirements
snp
HaplotypeCaller
vcf
gatk
updated 18 hours ago by
Ram
44k • written 22 hours ago by
cassandriatayfernandez
• 0
1
vote
0
replies
76
views
Dealing with indels in a fungal ITS2 MSA
indels
ITS2
MSA
alignment
21 hours ago by
Sergio A.S.
▴ 10
0
votes
1
reply
124
views
GPU-accelerated multiple sequence alignment tools
Multiple-Sequence-Alignment
updated 18 hours ago by
Ram
44k • written 22 hours ago by
jet
• 0
0
votes
1
reply
179
views
batch correction limma package (bead based assay data)
batch-correction
updated 1 day ago by
ATpoint
85k • written 2 days ago by
maria jose
• 0
1
vote
5
replies
368
views
WGCNA package.
RNA-seq
WGCNA
updated 1 day ago by
ATpoint
85k • written 2 days ago by
Jaber
▴ 20
0
votes
3
replies
206
views
Question on batch effect for a bulk RNA seq analysis
RNA-seq
batch-effect
13 hours ago by
akb
• 0
0
votes
0
replies
84
views
Paired splsda
splsda
updated 18 hours ago by
Ram
44k • written 1 day ago by
michelafrancesconi9
▴ 20
0
votes
3
replies
156
views
Mapping to transcriptome without gtf annotation
transcriptome
Mapping
assembly
updated 21 hours ago by
Michael
55k • written 1 day ago by
Vin Dee
• 0
0
votes
1
reply
130
views
Getting data from NCBI using Python
Ensembl
pyEnsembl
RNA-seq
updated 18 hours ago by
Ram
44k • written 1 day ago by
Quân
• 0
2
votes
6
replies
1.2k
views
Mapping all 32-mers within Hamming Distance = 3
hamming
alignment
kmer
ngs
short
updated 18 hours ago by
mourisl
▴ 30 • written 22 months ago by
giova34
▴ 10
0
votes
0
replies
85
views
How to work with Low allele Depth Variants in Strelka Variant caller
strelka
allelic-depth
low-GQX
updated 18 hours ago by
Ram
44k • written 1 day ago by
abhishekghadge
▴ 30
0
votes
1
reply
830
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta-analysis
METAL
GWAS
updated 1 day ago by
Ram
44k • written 18 months ago by
ymberzal
• 0
0
votes
0
replies
1.5k
views
METAL meta-analysis software crash
metal
meta-analysis
gwas
updated 1 day ago by
Ty
• 0 • written 4.5 years ago by
ydadmehr
• 0
1
vote
3
replies
202
views
cutadapt not working when calling in a bash code with qsub
qsub
trim
cutadpat
updated 1 day ago by
ATpoint
85k • written 1 day ago by
Meghan.T
• 0
2
votes
3
replies
194
views
Removing features from RNA assay in seurat
R
SEURAT
sc-RNA-Seq
updated 1 day ago by
yura.grabovska
▴ 520 • written 1 day ago by
Varun Gupta
★ 1.3k
0
votes
0
replies
95
views
News:
Eukaryotic Genome Assembly Using PacBio and Hi-C course (4-8 November)
Genome-Assembly
PacBio
Long-reads
Hi-C
1 day ago by
carlopecoraro2
★ 2.6k
0
votes
6
replies
941
views
miRNAseq - over-presented sequence in negative control
miRNAseq
adaptor
dimer
updated 1 day ago by
Ant
▴ 10 • written 13 months ago by
MH85
▴ 20
0
votes
0
replies
109
views
News:
Online Workshop - Bioinformatics Pipeline Development with Nextflow (November 13-15, 2024)
Workshop
Nextflow
RNA-Seq
1 day ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
99
views
Differential expression analysis from .chp files with Limma
expression
limma
IonTorrent
differential
1 day ago by
Rogerio Ribeiro
▴ 110
1
vote
2
replies
265
views
Genome Polishing nextPolish
nextpolish2
nextpolish
pilon
racon
18 hours ago by
Umer
▴ 110
0
votes
1
reply
197
views
co-occurrence matrix from my VCF file
co-occurrence
vcf
updated 1 day ago by
robben
• 0 • written 2 days ago by
HarperReed
• 0
2
votes
6
replies
1.6k
views
Center multiple pheatmap
pheatmap
patchwork
updated 1 day ago by
yura.grabovska
▴ 520 • written 3.8 years ago by
5utr
▴ 370
4
votes
3
replies
243
views
creat histogram in R
R
ggplot2
hist
updated 1 day ago by
Ram
44k • written 1 day ago by
G.S
▴ 60
2
votes
5
replies
279
views
constructing gene-based pangenome from orthofinder output file
orthofinder
pan-genome
updated 20 hours ago by
Dunois
★ 2.6k • written 2 days ago by
analyst
▴ 50
7
votes
6
replies
371
views
Genome Assembly Sorting
genome
assembly
sorting
updated 2 days ago by
GenoMax
146k • written 2 days ago by
Umer
▴ 110
0
votes
3
replies
291
views
Install PacBio lima via conda fails
conda
updated 2 days ago by
colindaven
6.8k • written 2 days ago by
michael.flower.14
▴ 200
1
vote
3
replies
228
views
human_variation_vcf
BaseRecalibrator
1 day ago by
runfreely2
• 0
2
votes
2
replies
237
views
How to interpret Eigengene dendrongram results
Eigengene
dendrogram
1 day ago by
nuorain
▴ 20
7
votes
24
replies
1.7k
views
GTF file
cellranger-arc
GTF
cellranger-arc-2.0.2
21 hours ago by
IrK
▴ 100
0
votes
6
replies
357
views
Explanation of DESeq factor leveling
DESeq
14 hours ago by
bthom
• 0
0
votes
1
reply
168
views
Allele frequency plot : imputed vs reference panel variants
imputation
genotyping
reference
updated 1 day ago by
BlastedBadger
▴ 160 • written 2 days ago by
hello_genome
• 0
0
votes
1
reply
187
views
rRNA contamination after filtering
QC
contamination
ribosomal-RNA
updated 2 days ago by
GenoMax
146k • written 2 days ago by
sleepystudent
• 0
119,074 results • Page
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Answer: How to extract all columns of CSQ using split-vep plugin of bcftools?
Answer: How to extract all columns of CSQ using split-vep plugin of bcftools?
Change STAR Parameters in rsem-calculate-expression
Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effects?
Dealing with indels in a fungal ITS2 MSA
Liftover using gVCF
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Recent Replies
Comment: How to use lme4() to perform differential expression on bulk RNA seq data with m
by
ATpoint
85k
Is it not possible to make the batch a fixed effect? If you google "edgeR / limma and lme4" you will find some posts over at Bioconductor w…
Answer: Questions Regarding Normalization and Standardization in RNA-seq Differential An
by
ATpoint
85k
In the bioinformatics field the term **normalization** describes the process to correct data (for example RNA-seq raw counts) for technical…
Comment: Can anyone share with me the R code for GSEA analysis?
by
GenoMax
146k
Any options here to get started: https://www.biostars.org/p/9504276/#9504292
Comment: all genes have negative logFC edgeR
by
rfran010
★ 1.3k
More details would be helpful, but it sounds like you are looking at the wrong comparison/contrast. For example, this is what I would see i…
Answer: extracting reads from FASTA/FASTQ file
by
GenoMax
146k
Use `bbduk.sh` from [BBMap suite][1] in `filter` mode. Guide available here : https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-…
Comment: Different annotations for different isoforms from the same gene
by
Chikae
• 0
Thank you very much for the comment! The differences in taxonomic annotations based on Blastx are substantial. The taxonomies listed in …
Comment: Aligning to transcriptome with STAR generates error in Salmon sequence length
by
Dunois
★ 2.6k
I think this stems from an issue with the `STAR` aligner (refer here [https://github.com/COMBINE-lab/salmon/issues/785][1] and links in the…
Comment: Different annotations for different isoforms from the same gene
by
Dunois
★ 2.6k
*How different* are these annotations exactly? Do these purported isoforms all have annotations that are still essentially from within the …
Comment: extracting reads from FASTA/FASTQ file
by
seidel
11k
Is there a reason you want to do this? A couple of ways to proceed. One way is to use your gene sequence as an alignment index, and then al…
Answer: DeSeq2 filter transcripts
by
seidel
11k
You can hand DESeq2 a matrix with rownames as gene names, or if the first column of your matrix is gene names use the tidy=TRUE argument (s…
Comment: Question on batch effect for a bulk RNA seq analysis
by
akb
• 0
Thank you, I have not tried the vst() method, but I did use removeBatchEffect when plotting the PCA and it did show correction of the batch…
Comment: Explanation of DESeq factor leveling
by
bthom
• 0
Thanks for sharing this! Would it be bad practice to reply to Mike's comment on bioconductor? I see that he had a possible explanation for …
Comment: Gnomad result tables column meaning.
by
Pierre Lindenbaum
164k
> y I recived a giant tsv file with variant calls first, you should ask the person who generated this file .
Comment: Trouble with Biopython residue depth
by
Wayne
★ 2.0k
Two suggestions: - After I download and unpack `msms` on a Linux system, I can run it with `./msms.x86_64Linux2.2.6.1`. I see the followin…
Comment: DESeq2: adjusted p-values become NA when sub-setting samples
by
GenoMax
146k
While we discourage cross-posting Mike Love does not stop by here often (has not bee here for 7 months as of now) so cross-posting on bioco…
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