Limit : this year
all time today this week this month this year
6,924 results • Page 2 of 139
Sort: replies
Rank Views Votes Replies
11
votes
22
replies
5.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 9 months ago by 44k • written 5.7 years ago by ▴ 280
15
votes
22
replies
12k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 9 months ago by 44k • written 7.5 years ago by ★ 1.4k
61
votes
22
replies
34k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 9 months ago by 44k • written 5.3 years ago by ▴ 540
163
votes
22
replies
19k
views
19 follow
Forum: Advice For Newcomers To The Bioinformatics Field
advice career
5 months ago by Medhat 9.8k
47
votes
22
replies
36k
views
17 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 7 months ago by • 0 • written 11.3 years ago by ★ 5.3k
14
votes
22
replies
6.4k
views
9 follow
Obtain chromosome, position, and alleles based on a list of SNP names
SNP
updated 6 months ago by 44k • written 6.8 years ago by ▴ 40
53
votes
21
replies
36k
views
17 follow
extract only geneID and gene symbol from GTF file
gtf python genome
updated 5 months ago by • 0 • written 9.7 years ago by ▴ 250
24
votes
21
replies
2.0k
views
6 follow
Tool: New Illumina error mode, new BBTools release (39.09) to deal with it
assembly NovaSeqX Illumina poly-G bbtools
updated 3 months ago by 148k • written 4 months ago by 20k
15
votes
21
replies
1.8k
views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
11 months ago by analyst ▴ 50
22
votes
21
replies
22k
views
7 follow
How To Rename FASTA Headers
FASTA Header
updated 14 days ago by 148k • written 8.1 years ago by ▴ 40
19
votes
21
replies
2.2k
views
7 follow
Help Choosing a Workstation for a New Bioinformatics Service
NGS hardware workstation
updated 4 months ago by 21k • written 4 months ago by • 0
15
votes
21
replies
6.6k
views
7 follow
alphafold online availability and use case
alphafold structure prediction
written 3.4 years ago by ▴ 70
20
votes
21
replies
14k
views
Run mutltiple Fastq files on Hisat2
Hisat2 hisat RNAseq
updated 3 months ago by 148k • written 8.2 years ago by ▴ 410
13
votes
21
replies
2.6k
views
Practical Haplotype Graph Paths
practical-haplotype-graph PHG
updated 11 months ago by ▴ 220 • written 14 months ago by ▴ 10
7
votes
20
replies
8.2k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 9 months ago by ▴ 230 • written 5.0 years ago by ▴ 80
2
votes
20
replies
2.0k
views
How to produce a single joint-called VCF file using as input three WGS samples (VCF,CRAM,FASTQ)
VCF WGS
updated 6 months ago by 44k • written 6 months ago by • 0
14
votes
20
replies
4.0k
views
6 follow
Clustering in single cell
seurat single-cell
12 weeks ago by Chris ▴ 340
18
votes
20
replies
5.1k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 9 months ago by 44k • written 8.3 years ago by ▴ 80
48
votes
20
replies
40k
views
16 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 4 months ago by ★ 1.3k • written 5.9 years ago by ▴ 70
5
votes
20
replies
4.9k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 9 months ago by 44k • written 7.0 years ago by ▴ 90
101
votes
19
replies
36k
views
19 follow
Tutorial: Heatmaps in R
heatmap R
updated 3 months ago by ▴ 50 • written 8.5 years ago by 27k
43
votes
19
replies
74k
views
14 follow
Forum: Will A Masters In Bioinformatics Help Me In Getting A Job?
education career
updated 6 months ago by 44k • written 13.8 years ago by ▴ 50
12
votes
19
replies
1.7k
views
Snakemake error
SnakeMake
10 weeks ago by aUser ▴ 70
75
votes
19
replies
4.5k
views
11 follow
Blog: A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 10 months ago by 4.5k • written 16 months ago by ▴ 30
12
votes
19
replies
15k
views
11 follow
SnpMatrix from VCF file
VCF Eqtl MatrixEQTL SnpMatrix vcftools
updated 10 months ago by ▴ 10 • written 7.9 years ago by ▴ 110
1
vote
19
replies
1.6k
views
Matching transcriptomic data to clinical data
R
updated 11 months ago by 44k • written 11 months ago by ▴ 10
90
votes
19
replies
33k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification expression bioconductor microarray machine-learning
5 months ago by Obi Griffith 20k
99
votes
19
replies
77k
views
13 follow
Sequence length from Fasta
fasta
updated 5 months ago by ▴ 140 • written 10.2 years ago by ▴ 90
12
votes
19
replies
1.9k
views
DESEQ with time series data on mutant vs. wild-type?
DESEQ
updated 3 months ago by ▴ 100 • written 3 months ago by ▴ 50
0
votes
19
replies
1.8k
views
Rstudio hangs on logisic regression using generalized estimating equations (geepack::geese())
geepack
6 months ago by jonas.andersson ▴ 40
3
votes
19
replies
2.4k
views
Systematic errors at the end and beginning of reads in NGS panels
sequencing NGS-panels
updated 6 months ago by 44k • written 18 months ago by ▴ 20
12
votes
19
replies
9.2k
views
how to identify CDR region in antibody sequence
CDR antibody
updated 10 months ago by • 0 • written 2.6 years ago by ▴ 50
5
votes
18
replies
1.9k
views
Forum: Is "training", fine tuning, or overfitting on "external independent validation datasets" considered cheating or scientific misconduct?
tools scientific misconduct overfitting
5 months ago by ivicts ▴ 10
6
votes
18
replies
6.3k
views
9 follow
Eigen genes using WGCNA
wgcna eigengenes
updated 7 months ago by • 0 • written 6.4 years ago by ▴ 120
70
votes
18
replies
147k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing samtools
updated 12 months ago by 165k • written 10.3 years ago by ▴ 880
8
votes
18
replies
2.8k
views
6 follow
How can I identify single-copy genes in a specific genome?
genome single-copy genes
updated 11 months ago by ★ 2.8k • written 11 months ago by ▴ 50
0
votes
18
replies
1.6k
views
Import list and assign distinct colors in R
R ggplot2
10 months ago by kmyers2 ▴ 90
13
votes
18
replies
12k
views
9 follow
Blastn, need help to increase speed
RNA-Seq blastn blast+
updated 8 months ago by ★ 2.8k • written 3.9 years ago by ▴ 20
146
votes
18
replies
37k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq alignment next-gen R assembly
updated 12 months ago by 44k • written 5.3 years ago by ▴ 850
2
votes
18
replies
2.5k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
9 months ago by b.contreras.moreira ▴ 370
11
votes
18
replies
2.0k
views
6 follow
Interpreting phylogenetics tree
phylogenetic-tree itol phylogenetics
updated 7 weeks ago by ★ 1.6k • written 4 months ago by ▴ 50
22
votes
18
replies
7.0k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 9 months ago by 44k • written 5.3 years ago by ★ 1.4k
1
vote
18
replies
1.2k
views
Submitting a job in parallel on slurm
bam slurm shell parallel
updated 5 months ago by ★ 1.3k • written 5 months ago by ▴ 10
35
votes
17
replies
17k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
R classification cancer randomForest machine-learning
5 months ago by Obi Griffith 20k
20
votes
17
replies
14k
views
17 follow
Best Practice On Variant Discovery For Bacteria?
updated 8 months ago by • 0 • written 12.6 years ago by 33k
1
vote
17
replies
1.5k
views
7 follow
The BUSCO assessment of the MAKER annotation results shows a low completeness
BUSCO MAKER
updated 6 weeks ago by 55k • written 11 weeks ago by • 0
12
votes
17
replies
7.2k
views
9 follow
ACMG assignment tools
wes acmg WES WGS
updated 9 months ago by • 0 • written 4.6 years ago by ▴ 190
11
votes
17
replies
6.8k
views
6 follow
ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data)
RNA-Seq R ESTIMATE
updated 3 months ago by • 0 • written 4.4 years ago by ▴ 10
6
votes
17
replies
7.2k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 9 months ago by 44k • written 10.3 years ago by ▴ 100
2
votes
17
replies
1.8k
views
RNA STAR and trimming
trimming STAR RNA-seq RNA
updated 6 months ago by 148k • written 6 months ago by ▴ 10
6,924 results • Page 2 of 139
Recent Votes
Creating pangenome graphs using vcf files?
Answer: STAR aligner - Is this still maintained?
Answer: Converting GP field in a VCF to GT
A: Extract subset of samples from multigenome vcf file
A: how to extract sample id with bcftools or vcftools
C: Extract uniquely mapped reads from bam file
Why some lines of BAM file do not contain NH tag
Recent Locations • All
Seattle, WA USA, 2 minutes ago
United Arab Emirates, 5 minutes ago
India, 8 minutes ago
United States, 14 minutes ago
Pakistan, 16 minutes ago
Australia, 17 minutes ago
Hong Kong, 22 minutes ago
Recent Awards • All
Popular Question to BerkeleyLab ▴ 70
Scholar to Buffo ★ 2.4k
Supporter to wenbinm ▴ 40
Popular Question to bioinfo ▴ 150
Scholar to Pierre Lindenbaum 165k
Popular Question to SethG • 0
Teacher to cmdcolin ★ 4.1k
Recent Replies
Answer: ChromHMM - annotation of chromatin states by Alex Reynolds 36k
Take a look at epilogos: https://epilogos.altius.org/ and https://github.com/meuleman/epilogos Disclaimer: I am involved in this project
Comment: constructing de novo assembly of plant short reads by analyst ▴ 50
Great, thanks!
Comment: chromHMM annotations by Bioinformatics_16 • 0
@i.sudbery Thank You
Answer: How to trim sequences by Mensur Dlakic ★ 28k
Generally speaking, your don't trim individual sequences. Rather, you align them first and then trim the alignment. I will give you links t…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam by samdegregori • 0
@mensur apologies on subjecting you to such a trivial troubleshooting error. Hitting myself on the head because I was thinking fa and fna w…
Comment: How to download metadata for the Broad Firehose RNA-seq data? by GenoMax 148k
You may want to get the data directly from GDC Portal/analysis center for the TCGA data: https://portal.gdc.cancer.gov/analysis_page?app=Pr…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam by Mensur Dlakic ★ 28k
I don't mean to sound harsh, but this is pretty basic stuff that is easily resolved if you read through the CheckM2 manual and follow the d…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam by samdegregori • 0
Yeah that's what I was thinking but triple checked and it seems to be right. And yes of course here is the output for reference: runnin…
Comment: Interpreting Varied Survival Times in TCGA-BRCA Data by mebius_band • 0
Sorry for interrupting your question but can I ask you where you find the data on what samples belong to healthy patients and what sample t…
Answer: Interpreting Varied Survival Times in TCGA-BRCA Data by wenbinm ▴ 40
I don't see why "samples with a survival outcome of 1" can't "have longer survival times than those where the survival outcome is 0"? Sampl…
Comment: gene annotation tool recommendations for oomycetes by GenoMax 148k
Oomycetes have pretty complex genomes (most of it repeats as I recall from working with one in distant past) so it would help a lot if you …
Comment: How to compare gene prediction by Mensur Dlakic ★ 28k
I think the first part of your advice is on point. However, I don't see the logic with this part: > One possible solution is to align all …
Answer: Web- based bioinformatics tool/s for identification of cysteine-rich proteins by Mensur Dlakic ★ 28k
There is a subset of BioPython called [**SeqIO**](https://biopython.org/wiki/SeqIO) with many examples of how to read and manipulate biolog…
Comment: constructing de novo assembly of plant short reads by Dave Carlson ★ 2.1k
You can just concatenate the various R1 and R2 fastq files before running the assembly. Let's say you have two samples (sample1, sample2),…
Comment: Reducing runtime of low-score alignments by Mensur Dlakic ★ 28k
Python is not very efficient for that type of work. There are all kinds of existing tools that are much faster: BLAST, FASTA and DIAMOND ar…
Traffic: 2804 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