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12,648 results • Page 3 of 253
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6
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25
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39k
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CluserProfiler message "No gene can be mapped"
R
updated 11 months ago by • 0 • written 6.2 years ago by ▴ 130
64
votes
24
replies
3.1k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 11 months ago by 43k • written 5.6 years ago by ▴ 80
87
votes
24
replies
24k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 4 weeks ago by • 0 • written 3.6 years ago by 3.2k
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 17 days ago by 19k • written 20 days ago by ▴ 580
15
votes
24
replies
2.6k
views
7 follow
Forum: Airport.bio: First class ticket to any biological database in the world
RNA-Seq ChIP-Seq SNP
updated 12 months ago by 43k • written 6.1 years ago by ▴ 350
27
votes
24
replies
2.5k
views
7 follow
Code Golf - bisulfite conversion
bisulfite bsseq code-golf
updated 11 months ago by 43k • written 5.6 years ago by 22k
20
votes
24
replies
7.0k
views
6 follow
Forum: Python or R
RNA-Seq alignment next-gen-sequencing
updated 12 months ago by 43k • written 6.0 years ago by ▴ 160
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp genotyping pathway gene enrichment
updated 7 months ago by 43k • written 14.2 years ago by 161k
4
votes
24
replies
6.1k
views
Split a concatenated alignment in multiple files
alignment fasta
updated 7 months ago by • 0 • written 9.2 years ago by ★ 2.8k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 6 months ago by 43k • written 14.1 years ago by 28k
159
votes
24
replies
63k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing splicing rna-seq
updated 11 months ago by 43k • written 11.2 years ago by 11k
48
votes
24
replies
8.3k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 10 months ago by 43k • written 6.8 years ago by ▴ 580
93
votes
23
replies
93k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by • 0 • written 5.8 years ago by ▴ 610
56
votes
23
replies
5.1k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 10 months ago by 43k • written 7.8 years ago by 14k
34
votes
23
replies
22k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq genome
updated 8 months ago by ▴ 120 • written 6.1 years ago by ▴ 680
6
votes
23
replies
26k
views
6 follow
devtools Installation error in R (version 3.5.3)?
github R phylogeny devtools
updated 11 months ago by 43k • written 5.1 years ago by ▴ 120
18
votes
23
replies
7.8k
views
7 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq genome cancer gene
updated 10 months ago by • 0 • written 6.5 years ago by ▴ 970
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp amino-acids
updated 4 months ago by ▴ 80 • written 12.4 years ago by ▴ 110
20
votes
23
replies
7.3k
views
6 follow
Tool: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq Windows Visualization ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 460
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
6 days ago by vytarasov ▴ 180
33
votes
23
replies
4.3k
views
8 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
updated 11 months ago by 22k • written 11 months ago by 4.2k
12
votes
23
replies
8.5k
views
6 follow
motif search with ATAC-seq
motif-search ATAC-seq
updated 11 months ago by 43k • written 5.6 years ago by ★ 2.6k
39
votes
23
replies
35k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 8 months ago by ▴ 40 • written 2.8 years ago by ▴ 130
6
votes
23
replies
1.5k
views
How to speed Salmon index up
metagenome genome salmon
4 months ago by young_bioinformatician ▴ 230
40
votes
23
replies
4.2k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 11 months ago by 43k • written 5.7 years ago by ▴ 110
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 4 weeks ago by 43k • written 5.4 years ago by ▴ 130
68
votes
23
replies
49k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 8 weeks ago by • 0 • written 6.5 years ago by ★ 1.2k
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 5 months ago by ★ 1.2k • written 11.2 years ago by ★ 1.3k
11
votes
23
replies
1.7k
views
gatk Hardfilter Error
hardfilter
updated 11 months ago by 54k • written 11 months ago by ▴ 30
66
votes
23
replies
11k
views
9 follow
Using Hdf5 To Store Bio-Data
hdf5 storage database
updated 7 months ago by 43k • written 14.2 years ago by 161k
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 5 weeks ago by 43k • written 5.1 years ago by ▴ 270
31
votes
22
replies
13k
views
6 follow
Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ SeqKit FASTA
updated 11 months ago by 43k • written 7.6 years ago by 8.5k
1
vote
22
replies
2.1k
views
error with Tximport when txOut = TRUE
tximport R
updated 10 months ago by 43k • written 10 months ago by • 0
28
votes
22
replies
58k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 10 months ago by • 0 • written 11.1 years ago by ▴ 90
26
votes
22
replies
14k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 12 months ago by 43k • written 7.3 years ago by 20k
57
votes
22
replies
29k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 6 weeks ago by 43k • written 4.6 years ago by ▴ 510
5
votes
22
replies
12k
views
sra toolkit program fastq-dump question.
sratoolkit fastq-dump
updated 10 months ago by 43k • written 9.3 years ago by ▴ 10
3
votes
22
replies
4.1k
views
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
GRanges
updated 10 months ago by ★ 2.2k • written 14 months ago by • 0
12
votes
22
replies
2.0k
views
Can anyone simplify GATK installation
GATK
4 months ago by Tundup • 0
34
votes
22
replies
3.0k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 11 months ago by 43k • written 4.0 years ago by ▴ 10
15
votes
22
replies
8.7k
views
What Are The Most Reliable Normalization Methods For Microarrays?
microarray
updated 6 months ago by 43k • written 14.2 years ago by 3.4k
24
votes
22
replies
27k
views
11 follow
replace fasta headers with another name in a text file
perl
updated 10 months ago by • 0 • written 9.9 years ago by ▴ 60
138
votes
22
replies
66k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 11 months ago by 88k • written 6.5 years ago by ★ 1.9k
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 4 weeks ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.6k
views
7 follow
Which New Bioinformatics Related Tool Would You Appreciate The Most?
programming
updated 10 months ago by 43k • written 11.8 years ago by 3.2k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 11 months ago by 43k • written 8.1 years ago by 13k
10
votes
21
replies
3.4k
views
How to interpret heatmap using plotheatmap from deeptools?
ATAC-seq deeptools
9 months ago by Chris ▴ 280
5
votes
21
replies
3.0k
views
How to get my tool on Homebrew ?
homebrew pipeline
updated 11 months ago by 43k • written 4.9 years ago by ▴ 20
39
votes
21
replies
14k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 11 months ago by 43k • written 5.6 years ago by 8.6k
80
votes
21
replies
37k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 6 months ago by • 0 • written 10.1 years ago by ▴ 660
12,648 results • Page 3 of 253
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Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
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
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Recent Replies
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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: 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.
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