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108,015 results • Page 1 of 2161
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1.2k
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205
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47k
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107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 21 days ago by ▴ 240 • written 11.9 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 38k • written 7.5 years ago by ★ 4.6k
716
votes
159
replies
105k
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
25k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 8 days ago by ▴ 240 • written 12.6 years ago by 11k
92
votes
105
replies
33k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 8 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 days ago by ▴ 10 • written 4.8 years ago by ▴ 260
318
votes
90
replies
211k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 4 months ago by 38k • 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
128
votes
83
replies
9.8k
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
5.5 years ago by Petr Ponomarenko ★ 2.7k
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 11 weeks ago by 38k • 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
164
votes
73
replies
54k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 14 months ago by 38k • written 11.6 years ago by ★ 1.8k
56
votes
72
replies
3.6k
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 6.3 years ago by ▴ 100 • written 6.3 years ago by ★ 4.1k
105
votes
72
replies
14k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 4.4 years ago by 11k • written 12.5 years ago by 11k
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 4 months ago by ▴ 20 • written 4.4 years ago by 84k
75
votes
70
replies
15k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 12 months ago by • 0 • written 5.0 years ago by 84k
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
biostar Forum
updated 16 months ago by 38k • written 8.8 years ago by 96k
279
votes
69
replies
17k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective Forum
updated 9 weeks ago by 38k • 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
134
votes
65
replies
3.4k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 12 months ago by 52k • written 3.2 years ago by ▴ 840
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 12 hours ago by 38k • written 10.0 years ago by 4.2k
34
votes
62
replies
4.0k
views
6 follow
Extract some features from a combined gene bank file in bash
gene sequence genome gene bank NCBI
updated 6.3 years ago by 38k • written 6.3 years ago by ★ 4.1k
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
144
votes
62
replies
9.3k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
biostar meta statistics Forum
updated 5.6 years ago by 52k • written 11.9 years ago by ★ 2.9k
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 day ago by 38k • written 7.8 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 8 days ago by 38k • written 9.7 years ago by 9.5k
26
votes
57
replies
5.9k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 2.1 years ago by 38k • written 4.3 years ago by ▴ 490
361
votes
57
replies
58k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 4 months ago by 84k • written 12.9 years ago by 96k
65
votes
57
replies
5.9k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 12 months ago by 38k • written 8.2 years ago by ▴ 20
145
votes
56
replies
7.3k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostar Forum
updated 9.7 years ago by 49k • written 9.9 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 38k • written 10.7 years ago by ▴ 380
41
votes
55
replies
9.6k
views
6 follow
hash function for DNA sequences
hash hashing DNA
6.8 years ago by midox ▴ 290
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 1 day ago by 38k • written 9.8 years ago by 9.5k
46
votes
54
replies
4.5k
views
12 follow
fasta seq header
sequence fasta
updated 5.9 years ago by 10k • written 5.9 years ago by ▴ 220
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
55
votes
53
replies
4.0k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria kraken spades blast sendsketch
updated 3.1 years ago by ▴ 30 • written 3.4 years ago by ▴ 200
113
votes
53
replies
4.8k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
career development authorship Forum
updated 3.8 years ago by ▴ 270 • written 3.8 years ago by ▴ 170
6
votes
53
replies
2.3k
views
how to download all sequences from web link
bash linux
3.6 years ago by Bioinfonext ▴ 430
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 38k • written 6.4 years ago by ★ 3.3k
54
votes
52
replies
43k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Tool on Gene Clustering Function based
updated 14 months ago by 38k • written 8.5 years ago by 7.4k
160
votes
52
replies
115k
views
28 follow
Fastq Convert To Fasta
perl
9.3 years ago by biolab ★ 1.4k
85
votes
52
replies
8.2k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 2.1 years ago by ▴ 120 • written 12.9 years ago by 3.4k
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 7 days ago by 38k • written 8.6 years ago by ▴ 320
88
votes
52
replies
44k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 14 months ago by ▴ 10 • written 5.2 years ago by ▴ 210
108,015 results • Page 1 of 2161
Recent Votes
Answer: command line - how to change name of multiple files at the same time
Answer: command line - how to change name of multiple files at the same time
Does a TCGA dataset need batch effect removal?
Answer: How to map and annotate gene symbols to gene type?
Answer: Visualization of Enrichment score for spatial 10x visium samples
Comment: How to map and annotate gene symbols to gene type?
Answer: command line - how to change name of multiple files at the same time
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Recent Replies
Comment: SNP calling by dthorbur ▴ 270
Okay, if I understand your comment correctly, GATK is behaving correctly. GATK has to fill all `GT` fields for any `POS` with at least 1 …
Comment: Tool to combine Germline Variant call from different variant callers by rohitsatyam102 ▴ 690
Hi @dlangenberger I have been using bcftools but I don't know how to get like a proportion value of how many variant callers support a par…
Comment: Differentially gene expression analysis by ATpoint 68k
Whst is unclear after reading the documentation?
Answer: exchange the monocle data with Seurat by fracarb8 ▴ 890
`exportCDS(monocle_object, export_to = 'Seurat', export_all = T)` Alternatively, you can directly use seurat with your normalise data. …
Comment: How I know the genome assembly quality by the low coverage Pacbio data ? by wdpang • 0
Thanks your anwser It's a rearrangement yeast, i only want to visual the mapping reads if complete and continuous. I will try your advice.
Comment: pileup consolidation tool by joe ▴ 380
I tried to use `Rsamtools::pileup()` but haven't been able to come up with the right parameters to pass in `PileupParam` ...maybe somewhere…
Comment: pileup consolidation tool by joe ▴ 380
Detection of RNA modifications.
Comment: pileup consolidation tool by Pierre Lindenbaum 152k
what is the scientific question you're trying to answer ?
Comment: Differentially gene expression analysis by Nai ▴ 20
I agree. Is it any tool to do so?
Comment: Differentially gene expression analysis by Nai ▴ 20
May you guide me for recount package?
Answer: Differentially gene expression analysis by Antonio R. Franco ★ 5.0k
If I am not wrong, DESeq2 heavily indicate that you need to use raw counts, not normalized counts.
Comment: Subbmission Data by GiV17 ▴ 40
I have the raw data, fastq files, but I didn’t want to submit them already, for further analysis I’m conducting, but I wanted to publish a …
Comment: Visualization of Enrichment score for spatial 10x visium samples by Omics data mining ▴ 210
Thanks. It worked.
Comment: Copy Number Variants, where to start? by Pierre Lindenbaum 152k
what did you find so far ?
Answer: docker build Command Works Yet It Does Not Create A Docker Container by ATpoint 68k
You created an image, not a container. See with `docker images`. As said in the other threads, please consider explaining the overall goal …
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