Limit : this year
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: replies
Rank Views Votes Replies
1.2k
votes
205
replies
47k
views
107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 17 days ago by ▴ 240 • written 11.8 years ago by 21k
234
votes
176
replies
83k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 3 months ago by 37k • written 7.5 years ago by ★ 4.6k
715
votes
159
replies
104k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training tutorial News handbook
updated 4 months ago by 1.5k • written 6.2 years ago by 96k
128
votes
122
replies
27k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 5 months ago by • 0 • written 4.3 years ago by 84k
296
votes
121
replies
24k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 3 days ago by ▴ 240 • written 12.5 years ago by 11k
92
votes
105
replies
32k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 3 days ago by ▴ 40 • written 4.4 years ago by 84k
59
votes
95
replies
14k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 4 hours ago by ▴ 10 • written 4.8 years ago by ▴ 260
318
votes
90
replies
210k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 4 months ago by 37k • written 12.0 years ago by 4.8k
76
votes
86
replies
24k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 6 weeks ago by 125k • written 6.2 years ago by 18k
100
votes
81
replies
23k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 5 months ago by 125k • written 6.1 years ago by ★ 1.8k
358
votes
79
replies
135k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 10 weeks ago by 37k • written 10.0 years ago by ★ 4.3k
116
votes
74
replies
41k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 3 months ago by 125k • written 12.2 years ago by ★ 3.2k
71
votes
71
replies
23k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot ggplot2 ggrepel bioconductor Tool
updated 3 months ago by ▴ 20 • written 4.4 years ago by 84k
279
votes
69
replies
17k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective Forum
updated 8 weeks ago by 37k • written 11.5 years ago by ▴ 160
142
votes
68
replies
42k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 7 months ago by • 0 • written 5.2 years ago by 84k
115
votes
66
replies
39k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
7 months ago by ATpoint 68k
306
votes
65
replies
19k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 4 months ago by 84k • written 12.9 years ago by 27k
284
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 4 months ago by 84k • written 11.9 years ago by 22k
38
votes
63
replies
17k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 24 days ago by 37k • written 10.0 years ago by 4.2k
157
votes
62
replies
73k
views
37 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 7 months ago by • 0 • written 11.9 years ago by 4.1k
72
votes
60
replies
22k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 9 weeks ago by • 0 • written 5.4 years ago by 84k
117
votes
59
replies
29k
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 1 hour ago by 37k • written 7.7 years ago by ▴ 30
205
votes
58
replies
38k
views
31 follow
Forum: Will Python Take The Place Of R?
biopython statistics r python Forum
updated 3 days ago by 37k • written 9.7 years ago by 9.5k
65
votes
57
replies
5.9k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 12 months ago by 37k • written 8.2 years ago by ▴ 20
361
votes
57
replies
57k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 4 months ago by 84k • written 12.9 years ago by 96k
109
votes
56
replies
39k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 4 months ago by 37k • written 10.7 years ago by ▴ 380
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 9 weeks ago by 37k • written 9.7 years ago by 9.5k
328
votes
54
replies
57k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 4 months ago by 84k • written 12.9 years ago by 24k
115
votes
52
replies
85k
views
21 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 3 days ago by 37k • written 8.6 years ago by ▴ 320
60
votes
52
replies
38k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 4 weeks ago by 37k • written 6.4 years ago by ★ 3.3k
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s fasta extract
updated 2 days ago by 37k • written 7.8 years ago by ▴ 600
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 4 months ago by 37k • written 12.3 years ago by ▴ 340
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 10 months ago by 37k • written 10.0 years ago by 33k
39
votes
48
replies
5.0k
views
CUTADAPT in windows
sequencing
updated 9 days ago by 37k • written 7.8 years ago by ★ 4.1k
261
votes
47
replies
20k
views
35 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 4 weeks ago by 37k • written 7.7 years ago by ★ 4.2k
106
votes
45
replies
79k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 5 months ago by ▴ 20 • written 10.5 years ago by ▴ 320
20
votes
45
replies
10k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq next-gen-sequencing
updated 10 days ago by 37k • written 7.7 years ago by ★ 1.1k
44
votes
44
replies
22k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq next-gen alignment
updated 4 months ago by 37k • written 8.8 years ago by ★ 1.5k
152
votes
44
replies
28k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 7 months ago by 37k • written 9.0 years ago by ★ 2.0k
90
votes
44
replies
57k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 9 months ago by 37k • written 11.8 years ago by ★ 3.4k
22
votes
44
replies
11k
views
How to remove contamination from the transcriptome assembly
RNA-Seq contamination assembly blast Hiseq reads
updated 5 months ago by 37k • written 7.2 years ago by ★ 1.7k
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 25 days ago by 37k • written 10.4 years ago by 20k
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome visualization ideogram
updated 4 months ago by 37k • written 12.9 years ago by ★ 1.6k
8
votes
42
replies
3.5k
views
NaS (Nanopore Synthetic-long) help
Assembly preprocessing
updated 4 weeks ago by 37k • written 7.7 years ago by ▴ 290
151
votes
42
replies
173k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 8 months ago by 37k • written 10.9 years ago by 20k
202
votes
41
replies
23k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 10 months ago by 37k • written 8.2 years ago by ★ 5.1k
23
votes
41
replies
12k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 11 weeks ago by • 0 • written 5.1 years ago by ▴ 110
166
votes
41
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence fasta
updated 3 days ago by • 0 • written 11.6 years ago by ▴ 240
16
votes
41
replies
7.6k
views
How to extract information from headers of fasta file
sequence
updated 7 months ago by 37k • written 7.9 years ago by ▴ 70
18
votes
41
replies
10k
views
6 follow
paired end illumina reads
Assembly paired end
updated 6 months ago by 37k • written 7.3 years ago by ▴ 290
1,000 results • Page 1 of 20
Recent Votes
Answer: Multiple sequence alignment of sequenecs of different length
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: Alien-hunter outputs
Answer: Annotating ENS codes to gene name
Comment: Annotating ENS codes to gene name
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
Recent Locations • All
United States, 3 minutes ago
Germany, 3 minutes ago
United Kingdom, 4 minutes ago
United States, 4 minutes ago
United States, 4 minutes ago
United States, 5 minutes ago
Palo Alto, CA, USA, 5 minutes ago
Recent Awards • All
Popular Question to Ankit ▴ 390
Popular Question to Hayler Edu ▴ 30
Popular Question to gokberk ▴ 70
Popular Question to gubrins ▴ 260
Teacher to natasha.sernova ★ 3.9k
Popular Question to Genotepes ▴ 950
Scholar to schlogl ▴ 130
Recent Replies
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files? by jv ▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs by schlogl ▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10 by ATpoint 68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file by ibq.enriquepola • 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe by Chris ▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file by barslmn ★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10 by Istvan Albert 96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10 by GenoMax 125k
> there is a massive difference in performance between them. It still is taking only one minute.
Comment: HTSeq error processing GFF file by ibq.enriquepola • 0
Yes, ![enter image description here][1] [1]: /media/images/76ecd9a7-10c2-4526-9849-062605ca
Answer: How can I convert this pairwise format to fasta? by GenoMax 125k
This seems to be the output from `sam2pairwise` program: https://github.com/mlafave/sam2pairwise A dirty way may be $ grep -A 1 ^M039…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe by Basti ★ 1.3k
EnhancedVolcano(CV.markers, x = "avg_log2FC", y = "p_val", lab = rownames(CV.markers), pCutoff = 1e-4, FCcutoff =…
Comment: How to perform multiple comparisons using edgeR? by ryandward • 0
Actually, you get one FDR per gene if you don't loop, and perform the comparisons all at once.
Comment: Remove duplicates in multifasta, where entries are paired by dthorbur ▴ 260
I don't have an existing tool that would do it, but if your fasta files aren't that large, it would be quite easy to do in R. You could cre…
Comment: How can I convert this pairwise format to fasta? by Shred ▴ 990
It's a SAM file. https://samtools.github.io/hts-specs/SAMv1.pdf For conversion https://www.biostars.org/p/129763/
Comment: Translating gene names to entrez id's by Ram 37k
While you're doing what @genomax says, please avoid `<pre><code>`. Use markdown (or the editor toolbar) instead.
Traffic: 2285 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