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12,709 results • Page 5 of 255
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12
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19
replies
5.8k
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how to identify CDR region in antibody sequence
CDR antibody
updated 11 weeks ago by • 0 • written 23 months ago by ▴ 50
93
votes
19
replies
60k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 11 months ago by 43k • written 13.7 years ago by ★ 2.6k
66
votes
19
replies
51k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 11 months ago by 43k • written 11.3 years ago by ★ 3.6k
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 10 months ago by 43k • written 11.0 years ago by ▴ 250
132
votes
19
replies
31k
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 3 months ago by 43k • written 4.6 years ago by ▴ 760
12
votes
19
replies
14k
views
11 follow
SnpMatrix from VCF file
VCF Eqtl MatrixEQTL SnpMatrix vcftools
updated 9 weeks ago by ▴ 10 • written 7.2 years ago by ▴ 110
28
votes
19
replies
15k
views
10 follow
How To Generate Mutations In Sequences Of A Fasta File?
fasta python mutation sequence
updated 10 months ago by 43k • written 12.7 years ago by ★ 1.5k
20
votes
19
replies
4.3k
views
7 follow
Bioinformatics word cloud to use in classes
teaching education
updated 11 months ago by 43k • written 5.2 years ago by ▴ 50
97
votes
19
replies
94k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc fasta sequence
updated 7 months ago by 43k • written 14.2 years ago by 28k
23
votes
19
replies
4.3k
views
7 follow
Tool: Big Browser : a new genom browser in development
genome-browser
updated 10 months ago by 43k • written 8.2 years ago by ★ 2.4k
38
votes
19
replies
11k
views
Tool: Excel add-in for DNA/RNA string manipulations
sequence DNA RNA Excel
updated 11 months ago by 43k • written 8.2 years ago by ▴ 140
19
votes
18
replies
15k
views
9 follow
vcf to bam
vcf bam
updated 10 months ago by ▴ 10 • written 8.6 years ago by ▴ 20
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 6 months ago by 43k • written 14.1 years ago by ★ 1.7k
21
votes
18
replies
1.8k
views
Forum: Is it safe to keep our data in github
github
updated 11 months ago by 43k • written 4.0 years ago by ▴ 70
68
votes
18
replies
131k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing samtools
updated 3 months ago by 161k • written 9.6 years ago by ▴ 870
23
votes
18
replies
1.5k
views
Forum: Versioning of Blast DB and Reproducible Research
database blast reproducible-research
updated 11 months ago by 43k • written 4.0 years ago by ▴ 60
39
votes
18
replies
6.1k
views
10 follow
Any Open Notebook Science In Bioinformatics?
open-notebook
updated 6 months ago by 43k • written 14.1 years ago by ▴ 380
2
votes
18
replies
1.7k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
6 weeks ago by b.contreras.moreira ▴ 200
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray annotation affymetrix probeset
updated 6 months ago by 43k • written 14.2 years ago by 18k
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome RNA-Seq sequencing
updated 8 months ago by 142k • written 8 months ago by ▴ 280
29
votes
18
replies
3.3k
views
7 follow
Forum: Should I quit PhD program?
education career research phd
updated 12 months ago by 43k • written 6.0 years ago by ▴ 30
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 11 months ago by 43k • written 7.7 years ago by 13k
29
votes
18
replies
2.7k
views
12 follow
Forum: what are the big questions in bioinformatics field nowadays
genome
updated 11 months ago by 43k • written 4.2 years ago by ▴ 20
10
votes
18
replies
1.4k
views
BedGraph file
bam BigWig
4 months ago by daffodil ▴ 10
9
votes
18
replies
6.5k
views
6 follow
10x 3' library creates R1 and R2 fastq files with the same read length
10x fastq scRNA-seq
updated 9 months ago by • 0 • written 22 months ago by ▴ 400
46
votes
18
replies
10.0k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 6 months ago by 43k • written 14.2 years ago by 3.4k
3
votes
18
replies
4.3k
views
how to identify TATA box in a gene list
TATA homer gene
updated 11 months ago by 43k • written 7.1 years ago by ★ 1.2k
0
votes
18
replies
1.1k
views
Import list and assign distinct colors in R
R ggplot2
9 weeks ago by kmyers2 ▴ 80
23
votes
18
replies
12k
views
7 follow
Fasta header trimming
sequence
updated 8 months ago by • 0 • written 7.3 years ago by ▴ 50
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 6 months ago by 43k • written 14.2 years ago by ▴ 390
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 29 days ago by 43k • written 4.6 years ago by ★ 1.4k
8
votes
18
replies
1.3k
views
6 follow
How can I identify single-copy genes in a specific genome?
genome single-copy genes
updated 3 months ago by ★ 2.5k • written 3 months ago by ▴ 50
14
votes
18
replies
2.4k
views
Clustering in single cell
seurat single-cell
updated 7 months ago by ▴ 210 • written 7 months ago by ▴ 280
26
votes
18
replies
8.6k
views
10 follow
Indexing Compressed Fastq-Like Data
fastq
updated 10 months ago by 43k • written 13.8 years ago by ★ 5.1k
27
votes
17
replies
22k
views
8 follow
BioPython: convert fasta to fastq without quality score input file
parsing phred fasta BioPython fastq
updated 11 months ago by • 0 • written 10.0 years ago by 5.8k
6
votes
17
replies
1.7k
views
MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 MacOS
updated 11 months ago by 43k • written 12 months ago by ▴ 190
7
votes
17
replies
5.1k
views
Tool: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
RNA-Seq sequencing
updated 10 months ago by 43k • written 5.7 years ago by ▴ 80
20
votes
17
replies
3.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by ★ 1.2k • written 3.3 years ago by ▴ 110
36
votes
17
replies
3.7k
views
9 follow
Which Software Development Technique Is Used In Your Lab?
subjective
updated 6 months ago by 43k • written 14.2 years ago by 28k
17
votes
17
replies
2.0k
views
6 follow
Forum: Journal for beginners
journal
updated 12 months ago by 43k • written 6.2 years ago by ▴ 20
6
votes
17
replies
5.6k
views
8 follow
Eigen genes using WGCNA
wgcna eigengenes
updated 11 months ago by ▴ 40 • written 5.7 years ago by ▴ 120
6
votes
17
replies
6.7k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 4 weeks ago by 43k • written 9.6 years ago by ▴ 100
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 11 months ago by 43k • written 5.3 years ago by 88k
0
votes
17
replies
3.0k
views
Processing Fast5 files from ONT for direct RNA
Nanopore Nanopolish ELIGOS2 Fast5 Tombo
updated 10 months ago by ▴ 50 • written 17 months ago by • 0
4
votes
17
replies
1.4k
views
7 follow
How to edit a fq.gz file
fastq
updated 4 months ago by 100k • written 4 months ago by • 0
22
votes
17
replies
4.0k
views
Tool: epic: new ChIP-Seq caller based on the SICER algorithm
ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 960
38
votes
17
replies
3.3k
views
7 follow
Forum: Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
sam bam samtools
updated 11 months ago by 43k • written 3.7 years ago by ▴ 250
17
votes
17
replies
21k
views
13 follow
How To Efficiently Sort A Fastq File By Entry Id?
fastq illumina sort next-gen-sequencing alignment
updated 4 months ago by 43k • written 12.5 years ago by ▴ 840
10
votes
17
replies
1.9k
views
Building reference dbSNP file using WGS samples
NGS WGS Variant-calling non-model Bootstrapping
5 months ago by analyst ▴ 50
9
votes
17
replies
2.6k
views
Interpret plots from DiffBind
DiffBind
updated 9 months ago by ★ 2.0k • written 11 months ago by ▴ 280
12,709 results • Page 5 of 255
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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Recent Replies
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
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