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1,000 results • Page 1 of 20
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1.2k
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206
replies
50k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 days ago by ★ 1.2k • written 12.2 years ago by 21k
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 days ago by 39k • written 7.8 years ago by ★ 4.6k
744
votes
162
replies
114k
views
101 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 5 weeks ago by 1.8k • written 6.5 years ago by 98k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
298
votes
121
replies
26k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 4 months ago by ▴ 260 • written 12.9 years ago by 11k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 weeks ago by 39k • written 4.8 years ago by 85k
59
votes
95
replies
15k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 4 months ago by ▴ 10 • written 5.1 years ago by ▴ 260
323
votes
90
replies
219k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 8 months ago by 39k • written 12.4 years ago by 4.9k
76
votes
86
replies
26k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 5 months ago by 129k • written 6.5 years ago by 18k
128
votes
83
replies
10k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
fastq compressor lossless fastq compression Tool
5.9 years ago by Petr Ponomarenko ★ 2.7k
102
votes
81
replies
25k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 9 months ago by 129k • written 6.4 years ago by ★ 1.9k
360
votes
81
replies
138k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
6 weeks ago by ole.tange ★ 4.3k
117
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 7 months ago by 129k • written 12.5 years ago by ★ 3.3k
56
votes
72
replies
4.0k
views
8 follow
Dear biostars I really need your kindly help, please save me from this hardship situation
software error mirddep2 perl miRNAs RNA-Seq
updated 6.6 years ago by ▴ 100 • written 6.7 years ago by ★ 4.2k
105
votes
72
replies
14k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 4.7 years ago by 11k • written 12.9 years ago by 11k
71
votes
71
replies
25k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot ggplot2 ggrepel bioconductor Tool
updated 8 months ago by ▴ 40 • written 4.8 years ago by 85k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 11 weeks ago by 39k • written 5.3 years ago by 85k
164
votes
70
replies
56k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.4 years ago by ▴ 430 • written 11.9 years ago by ★ 1.8k
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 3 months ago by 39k • written 9.1 years ago by 98k
279
votes
69
replies
18k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 3 months ago by 39k • written 11.8 years ago by ▴ 160
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 11 weeks ago by 39k • written 4.9 years ago by 72k
134
votes
65
replies
3.9k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 16 months ago by 52k • written 3.5 years ago by ▴ 880
306
votes
65
replies
20k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 8 months ago by 85k • written 13.3 years ago by 27k
286
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 8 months ago by 85k • written 12.2 years ago by 22k
160
votes
63
replies
76k
views
38 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 4 days ago by 39k • written 12.2 years ago by 4.1k
38
votes
63
replies
17k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 3 months ago by 39k • written 10.3 years ago by 4.2k
144
votes
62
replies
9.6k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 3 months ago by 39k • written 12.3 years ago by ★ 2.9k
34
votes
62
replies
4.4k
views
6 follow
Extract some features from a combined gene bank file in bash
gene sequence genome gene bank NCBI
updated 6.6 years ago by 39k • written 6.6 years ago by ★ 4.2k
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
117
votes
59
replies
30k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 3 months ago by 39k • written 8.1 years ago by ▴ 30
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
65
votes
57
replies
6.3k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 16 months ago by 39k • written 8.6 years ago by ▴ 20
26
votes
57
replies
6.4k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 2.4 years ago by 39k • written 4.7 years ago by ▴ 510
361
votes
57
replies
61k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 8 months ago by 85k • written 13.3 years ago by 98k
145
votes
56
replies
7.5k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 3 months ago by 39k • written 10.2 years ago by 98k
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 8 months ago by 39k • written 11.0 years ago by ▴ 380
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 3 months ago by 39k • written 10.1 years ago by 9.6k
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.2 years ago by midox ▴ 290
328
votes
54
replies
58k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 8 months ago by 85k • written 13.2 years ago by 24k
46
votes
54
replies
5.1k
views
12 follow
fasta seq header
sequence fasta
updated 6.3 years ago by 10k • written 6.3 years ago by ▴ 220
55
votes
53
replies
4.7k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria kraken spades blast sendsketch
updated 3.5 years ago by ▴ 30 • written 3.7 years ago by ▴ 200
120
votes
53
replies
90k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 11 weeks ago by • 0 • written 9.0 years ago by ▴ 330
6
votes
53
replies
2.6k
views
how to download all sequences from web link
bash linux
3.9 years ago by Bioinfonext ▴ 430
113
votes
53
replies
5.2k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 5 days ago by 39k • written 4.2 years ago by ▴ 170
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 3.3k
85
votes
52
replies
8.5k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 2.5 years ago by ▴ 130 • written 13.2 years ago by 3.4k
54
votes
52
replies
45k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Tool on Gene Clustering Function based
updated 17 months ago by 39k • written 8.8 years ago by 7.5k
88
votes
52
replies
46k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 18 months ago by ▴ 10 • written 5.6 years ago by ▴ 210
160
votes
52
replies
119k
views
28 follow
Fastq Convert To Fasta
perl
9.6 years ago by biolab ★ 1.4k
1,000 results • Page 1 of 20
Recent Votes
Comment: Getting species names and taxa id from assembly accession number
Comment: STAR GenomeIndex output (which is the BAM file?)
Answer: [Meta] Use of AI
Answer: h5ad cellxgene to R
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
Answer: Rna-Seq Pipeline
Comment: Create customized gene annotation file
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Recent Replies
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth? by Trivas ★ 1.1k
Your issue is with your bed file then, not necessarily with deep tools. I'd look into the bedtools suite to see if you can minimize overlap…
Comment: variant allelic fraction by Pierre Lindenbaum 154k
https://www.biostars.org/p/492331/
Comment: variant allelic fraction by malm • 0
ok how can i calculate it from the vep file?
Comment: Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads by benformatics 3.6k
I think it would be fair (and conservative) to remove read pairs where one maps to the mitochondrial genome. It should be a relatively very…
Answer: Convert Bam file to Fastq by Michael 52k
I think your code is incorrect bash syntax. I think you want something like this: sort bam_headers.txt > bam_haeders-sorted.txt # c…
Comment: Combination of ROC CURVE by Maria17 ▴ 20
For example, if three targets are combined and the mean value is plotted, the different combinations give different numbers, but there are …
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental by Kermit ▴ 80
neither simple nor helpful, but perhaps the OP changed his question away from "why might diff models produce diff results" to the current "…
Comment: Convert Bam file to Fastq by Michael 52k
At first, I would trust samtools to do the right thing but of course it doesn't hurt to double check. But I think the crux is what is in fa…
Comment: Convert Bam file to Fastq by Pierre Lindenbaum 154k
paste fastq1_read_ids.txt fastq2_read_ids.txt is a tabular file with two column. Is it the same for bam_read_names.txt ?
Comment: variant allelic fraction by Pierre Lindenbaum 154k
this is not a field provided by VEP.
Answer: WGCNA Trait File Issues by Jennifer M • 0
![enter image description here][1] [1]: /media/images/0cf4eaa7-9550-4bbb-b43e-208dc787
Comment: Pairwise Alignment by WouterDeCoster 47k
> for whole genome analysis What do you mean with that? You provide too little information for us to answer your question.
Comment: Getting species names and taxa id from assembly accession number by GenoMax 129k
There must be some temporary glitch. Following command works (via EntrezDirect): $ esearch -db assembly -query GCA_000001405.29 | esu…
Comment: h5ad cellxgene to R by abmmki • 0
matrix=adata.X.toarray() feature_names = adata.var['feature_name'] pd.DataFrame(data=matrix, index=adata.obs_names, c…
Comment: h5ad cellxgene to R by abmmki • 0
I am trying use the same data and same method. But when I read the csv expression matrix in R, it frozen. Could you share your final seurat…
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