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13,334 results • Page 2 of 267
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85
votes
23
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 2 days ago by • 0 • written 3.5 years ago by 3.2k
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 5 months ago by 43k • written 14.1 years ago by 3.4k
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 months ago by • 0 • written 8.1 years ago by 20k
83
votes
34
replies
18k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 10 months ago by • 0 • written 5.8 years ago by ★ 1.3k
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 9 months ago by ▴ 30 • written 13.4 years ago by ▴ 470
82
votes
46
replies
8.6k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 4 weeks ago by 4.2k • written 10 months ago by ▴ 830
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq atac-seq normalization
updated 13 days ago by • 0 • written 4.3 years ago by ▴ 240
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 7 months ago by ▴ 210 • written 10.2 years ago by ▴ 750
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 5 months ago by 43k • written 14.1 years ago by 13k
80
votes
21
replies
36k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by • 0 • written 10.0 years ago by ▴ 660
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 5 months ago by 43k • written 14.0 years ago by 28k
79
votes
35
replies
9.6k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 10 months ago by • 0 • written 8.4 years ago by ▴ 650
79
votes
86
replies
31k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 10 months ago by 43k • written 7.4 years ago by 20k
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 6 weeks ago by ▴ 60 • written 7.8 years ago by 6.5k
76
votes
14
replies
12k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 10 months ago by 43k • written 6.9 years ago by ★ 3.4k
76
votes
26
replies
119k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 4 months ago by ★ 2.8k • written 9.0 years ago by ▴ 260
75
votes
19
replies
3.4k
views
11 follow
Blog: A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 6 weeks ago by 4.2k • written 7 months ago by ▴ 30
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 5 months ago by 43k • written 14.0 years ago by 161k
74
votes
16
replies
4.7k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
subjective
updated 9 months ago by 43k • written 13.1 years ago by ★ 3.3k
73
votes
14
replies
4.2k
views
12 follow
Forum: Things you wish you knew when entering the bioinformatics field
pitfalls advice
updated 10 months ago by 43k • written 3.6 years ago by ★ 16k
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by • 0 • written 10.2 years ago by 100k
72
votes
71
replies
31k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 10 months ago by 43k • written 5.6 years ago by 87k
71
votes
15
replies
48k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
written 6.0 years ago by ▴ 420
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 4 weeks ago by ★ 1.2k • written 5.1 years ago by 16k
69
votes
25
replies
7.0k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 5 months ago by 43k • written 14.1 years ago by ▴ 190
69
votes
39
replies
4.5k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 11 months ago by 43k • written 6.9 years ago by 13k
68
votes
18
replies
129k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing samtools
updated 11 weeks ago by 161k • written 9.5 years ago by ▴ 870
68
votes
48
replies
8.7k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 11 months ago by 43k • written 6.8 years ago by 100k
68
votes
25
replies
15k
views
12 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 5 months ago by 141k • written 5.1 years ago by ★ 1.4k
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline next-gen-sequencing rna rna-seq
updated 11 months ago by 43k • written 13.9 years ago by 24k
66
votes
23
replies
49k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 4 weeks ago by • 0 • written 6.4 years ago by ★ 1.2k
66
votes
19
replies
50k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 10 months ago by 43k • written 11.2 years ago by ★ 3.6k
66
votes
23
replies
10k
views
9 follow
Using Hdf5 To Store Bio-Data
hdf5 storage database
updated 6 months ago by 43k • written 14.1 years ago by 161k
65
votes
15
replies
14k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 10 months ago by 43k • written 5.5 years ago by 16k
65
votes
10
replies
3.4k
views
6 follow
Incentive For Learning Emboss
emboss
updated 9 months ago by 43k • written 13.0 years ago by 11k
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp genotyping pathway gene enrichment
updated 6 months ago by 43k • written 14.1 years ago by 161k
64
votes
24
replies
3.0k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 10 months ago by 43k • written 5.5 years ago by ▴ 80
62
votes
14
replies
195k
views
9 follow
How To Deal With Duplicate Row Names Error In R
r
updated 11 months ago by 11k • written 11.2 years ago by ▴ 910
61
votes
23
replies
56k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 4 months ago by ★ 1.2k • written 11.1 years ago by ★ 1.3k
61
votes
51
replies
22k
views
9 follow
Tool: Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff sequence fastq next-gen
updated 9 months ago by 43k • written 10.0 years ago by ▴ 790
61
votes
14
replies
11k
views
11 follow
Recommend Easy To Use Microarray Clustering Software
microarray clustering
updated 6 months ago by 43k • written 14.6 years ago by 100k
60
votes
21
replies
3.8k
views
14 follow
Reproduce the article "The complete sequence of a human genome."
genome assembly
updated 7 months ago by 54k • written 7 months ago by ▴ 60
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general subjective
updated 6 months ago by 43k • written 14.2 years ago by 28k
59
votes
25
replies
5.4k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size statistical-power RNA-Seq
updated 10 months ago by 43k • written 3.7 years ago by ▴ 220
58
votes
8
replies
8.3k
views
8 follow
What is the best way to combine machine learning algorithms for feature selection such as Variable importance in Random Forest with differential expr…
RNA-Seq rna-seq
updated 6 months ago by • 0 • written 6.1 years ago by ▴ 150
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 5 months ago by 43k • written 14.0 years ago by 18k
57
votes
15
replies
6.2k
views
9 follow
Forum: Good practices while dealing with very large datasets
Big-Data Programming
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.2k
57
votes
35
replies
14k
views
9 follow
How to get sample names and genotype for SNP in multi-sample VCF file
SNP genotype GATK
updated 6 months ago by 87k • written 6.2 years ago by ▴ 520
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat DESeq2 Batch-Effect
updated 10 days ago by 43k • written 4.5 years ago by ▴ 510
56
votes
52
replies
49k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 10 months ago by 43k • written 9.7 years ago by 7.5k
13,334 results • Page 2 of 267
Recent Votes
Comment: Bioinformatics_where do i start
Answer: Bwa sampe - BGI
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
A: Code golf: detecting homopolymers of length N in the (human) genome
Code golf: detecting homopolymers of length N in the (human) genome
Answer: WGCNA network from Adjacency or TOM matrix
A: What Are The Most Common Stupid Mistakes In Bioinformatics?
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Recent Replies
Comment: add INFO tag to vcf with bcftools by Javier • 0
Hi, im traying to do something similar, could you share the code to do what you describe. Thanks
Comment: Visualization of PROKKA Annotation Result? by Joe 21k
Colin's answer is essentially the right one I believe, but the more immediate consideration is: *what are you actually trying to show?* Mo…
Comment: Bioinformatics_where do i start by Pierre Lindenbaum 161k
https://www.biostars.org/p/9554614/ ; https://www.biostars.org/p/98983 ; https://www.biostars.org/p/9583727/ :https://www.biostars.org/p/4…
Answer: Bwa sampe - BGI by Pierre Lindenbaum 161k
bwa sampe produces unsorted SAM , not BAM. converting SAM to BAM will reduce the size sorting the BAM will reduce the size (you can …
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Bikram Kumar • 0
Hi! Should I delete the stack exchange post? I didn't know that cross posting is bad. [https://meta.stackoverflow.com/a/425789/5140632][1] …
Answer: Visualization of PROKKA Annotation Result? by colindaven 6.3k
You need a genome browser and you can probably use GBK or gff3 format. Here are some suggestions - I like JBrowse best, Artemis in its …
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Pierre Lindenbaum 161k
cross-posted https://bioinformatics.stackexchange.com/questions/22401
Comment: Tumour purity and ploidy estimation by bp22 ▴ 60
Hi Llyod98, This issue is still unresolved and I have not been able to find a tool or solution for purity and ploidy estimation when ther…
Comment: Ensembl gene id conversion by ATpoint 81k
Can you add some examples. It is hard to debug textual descriptions.
Answer: Which experiments generate Position Frequency Matrix? by ATpoint 81k
Yes, ChIP-seq or similar methods that assay the DNA binding of a protein. But for a reliable matrix you don't need one or two but many data…
Comment: Statistical Advice Needed for RNAseq Data Analysis by ATpoint 81k
> ensuring it's not merely a product of random chance If your approach of getting DEGs is a proper and sound one (e.g. DESeq2 or limma) th…
Comment: Can I compare kallisto counts from samples with different amount of reads? by ATpoint 81k
Unequal numbers of reads are normal, that is why normalization is needed. If you want to do simple analysis such as number of detected gene…
Comment: Error in edgeR/Deseq2 Analysis by ATpoint 81k
Please ask at https://help.galaxyproject.org/ which is the Galaxy help forum.
Comment: RNAseq 1 control 2 different treatment by matteo.levorato • 0
yes, this is what I did. However, since my treatments are very similar each other, when I check upregulated genes in one treatment, they ar…
Comment: snakemake output directory by 进 • 0
it is right answer
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