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Limit : all time
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1,000 results • Page
3 of 20
Sort: replies
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Votes
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78
votes
42
replies
29k
views
25 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 27 days ago by
Ram
39k • written 9.6 years ago by
Irsan
★ 7.7k
122
votes
42
replies
9.0k
views
21 follow
News:
Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
meta
biostars
updated 3 months ago by
Ram
39k • written 10.5 years ago by
Istvan Albert
98k
151
votes
42
replies
176k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap
r
updated 12 months ago by
Ram
39k • written 11.3 years ago by
Obi Griffith
20k
57
votes
42
replies
5.3k
views
12 follow
Forum:
Why is academic software hard to install?
software-installation
updated 16 months ago by
Ram
39k • written 8.6 years ago by
lh3
33k
8
votes
42
replies
3.8k
views
NaS (Nanopore Synthetic-long) help
Assembly
preprocessing
updated 5 months ago by
Ram
39k • written 8.0 years ago by
midox
▴ 290
11
votes
42
replies
3.0k
views
over presented kmer in fastq
fastqc
RNA-Seq
5.6 years ago by
Sam
▴ 150
31
votes
41
replies
1.6k
views
12 follow
Forum:
Question regarding journal publications
journals
publications
Forum
3.3 years ago by
K.Gee
▴ 40
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 3 months ago by
Ram
39k • written 8.6 years ago by
William
★ 5.2k
5
votes
41
replies
2.0k
views
Insert sequence in nt database
nt
3.0 years ago by
anasofiamoreira94
▴ 80
98
votes
41
replies
4.6k
views
17 follow
Forum:
I am really pissed off by the bioinformatics software world. Do/can we have a better solution?
software-error
next-gen-sequencing
updated 8 weeks ago by
Ram
39k • written 6.8 years ago by
moxu
▴ 500
18
votes
41
replies
11k
views
6 follow
paired end illumina reads
Assembly
paired end
updated 10 months ago by
Ram
39k • written 7.6 years ago by
midox
▴ 290
23
votes
41
replies
2.5k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS
biopython
illumina
WGS
updated 25 days ago by
Ram
39k • written 6 weeks ago by
Vijith
▴ 30
38
votes
41
replies
50k
views
9 follow
Volcano Plot from DEseq2
R
written 5.6 years ago by
1769mkc
★ 1.1k
13
votes
41
replies
1.7k
views
Is my file created completely
sam
BWA-MEM
BWA
updated 10 weeks ago by
Ram
39k • written 6.1 years ago by
micro32uvas
▴ 10
19
votes
41
replies
7.4k
views
7 follow
n.sv number for batch effects in RNA-seq
RNA-Seq
updated 5.8 years ago by
ivivek_ngs
★ 5.2k • written 5.8 years ago by
sophialovechan
▴ 80
167
votes
41
replies
88k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 4 months ago by
Onur
• 0 • written 12.0 years ago by
Palu
▴ 240
16
votes
41
replies
7.9k
views
How to extract information from headers of fasta file
sequence
updated 11 months ago by
Ram
39k • written 8.2 years ago by
Crystal
▴ 70
24
votes
41
replies
13k
views
10 follow
WGCNA modules and categorical traits relationship
WGCNA
updated 6 months ago by
lovelymaoqin
• 0 • written 5.4 years ago by
BrunoGiotti
▴ 120
18
votes
40
replies
16k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 11 weeks ago by
Ram
39k • written 6.9 years ago by
Esaie
▴ 170
68
votes
40
replies
5.0k
views
11 follow
Can We Agree On A Short Twitter Hashtag For Nextgen Sequencing?
next-gen
sequencing
sequencing
updated 11.6 years ago by
pmenzel
▴ 310 • written 11.6 years ago by
Samuel Lampa
★ 1.3k
10
votes
40
replies
5.2k
views
weird insert size post trimming
RNA-Seq
updated 5.8 years ago by
Gabriel R.
★ 2.9k • written 5.8 years ago by
badribio
▴ 280
16
votes
40
replies
4.9k
views
About TCGA CNV data preprocessing
SNP
CNV
updated 4.6 years ago by
Kevin Blighe
85k • written 4.6 years ago by
Eric Wang
▴ 40
67
votes
40
replies
8.3k
views
12 follow
Forum:
I want to re-open the old debate: python or perl ?
perl
python
updated 15 months ago by
Ram
39k • written 8.5 years ago by
Gabriel R.
★ 2.9k
6
votes
40
replies
9.3k
views
Fastx_Collapser Has No Fastq Output
fastx
RNA-seq
updated 3 months ago by
Ram
39k • written 9.7 years ago by
nbvasani
▴ 240
40
votes
40
replies
9.6k
views
9 follow
What is the reason for trimming reads to 30 bp for ATAC-seq aligning?
ATAC-seq
alignment
updated 5.3 years ago by
Kevin Blighe
85k • written 6.7 years ago by
datascientist28
▴ 540
151
votes
39
replies
23k
views
20 follow
Forum:
A Farewell To Bioinformatics
bioinformatics
updated 3 months ago by
Ram
39k • written 10.4 years ago by
Martin A Hansen
3.0k
20
votes
39
replies
8.1k
views
7 follow
Is Blast+ Running As Fast As It Could ?
blast
blast
memory
updated 7.7 years ago by
Kumar
▴ 160 • written 11.4 years ago by
Amr
▴ 160
226
votes
39
replies
282k
views
33 follow
Gene Id Conversion Tool
mapping
conversion
updated 9 months ago by
Ram
39k • written 13.6 years ago by
Renee
▴ 620
11
votes
39
replies
3.1k
views
Any advice for a de novo genome assembly
k-mer
de novo
genome
assembly
updated 6.5 years ago by
krsahlin
▴ 60 • written 6.5 years ago by
Picasa
▴ 640
25
votes
39
replies
4.7k
views
8 follow
Forum:
Bioinformatics Study Group
study-group
updated 3 months ago by
Ram
39k • written 9.9 years ago by
Olivier
▴ 440
277
votes
39
replies
168k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 10 weeks ago by
Ram
39k • written 8.8 years ago by
Obi Griffith
20k
91
votes
39
replies
134k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 weeks ago by
Dan
▴ 120 • written 10.9 years ago by
abi
▴ 370
36
votes
39
replies
2.9k
views
11 follow
Forum:
Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast
RNA-Seq
alignment
next-gen-sequencing
updated 18 days ago by
Ram
39k • written 5.6 years ago by
dhbradshaw
▴ 130
18
votes
39
replies
3.0k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 13 days ago by
Ram
39k • written 4.1 years ago by
chernouhov sergey
▴ 50
69
votes
39
replies
3.4k
views
14 follow
Forum:
Preparation for Bioinformatics.SE closing
meta
biostars
updated 23 days ago by
Ram
39k • written 6.0 years ago by
John
13k
66
votes
39
replies
6.5k
views
13 follow
What Do You Consider The Most Trivial And The Most Challenging Tasks In Your Particular Field Of Work?
career
subjective
updated 2.2 years ago by
Ram
39k • written 13.2 years ago by
Marcos De Carvalho
▴ 310
81
votes
39
replies
6.2k
views
11 follow
News:
State Of Biostar - Future Directions (January 2013)
biostars
updated 3 months ago by
Ram
39k • written 10.4 years ago by
Istvan Albert
98k
55
votes
39
replies
4.7k
views
8 follow
Programming Challenge - Synthetic Whole Genome Vcf
vcf
python
perl
awk
updated 10.7 years ago by
Rm
8.2k • written 10.8 years ago by
Mahdi Sarmady
▴ 310
39
votes
38
replies
7.2k
views
9 follow
DNA composition - all k-mers and their frequency in some sequencing data
sequencing
updated 9 months ago by
Ram
39k • written 7.6 years ago by
John
13k
48
votes
38
replies
15k
views
8 follow
Forum:
Eukaryotic Genome Annotation in 2016
software
genome
annotation
updated 8 weeks ago by
Ram
39k • written 7.2 years ago by
Eric Normandeau
11k
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 13 months ago by
Ram
39k • written 8.3 years ago by
Mo
▴ 920
100
votes
38
replies
28k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 27 days ago by
Jeremy Leipzig
21k • written 9.6 years ago by
14134125465346445
★ 3.6k
224
votes
38
replies
136k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 5 months ago by
harelarik
▴ 90 • written 10.3 years ago by
Malachi Griffith
19k
129
votes
38
replies
5.9k
views
21 follow
Forum:
Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 5 days ago by
Ram
39k • written 4.2 years ago by
Istvan Albert
98k
27
votes
38
replies
17k
views
Heatmap based with FPKM values
RNA-Seq
next-gen
R
updated 4.1 years ago by
Biostar
20 • written 5.5 years ago by
Mehmet
▴ 800
53
votes
38
replies
3.5k
views
10 follow
Multiple alignment software
alignment
clustal omega
tcoffee
updated 3.7 years ago by
Istvan Albert
98k • written 3.7 years ago by
juanjo75es
▴ 130
47
votes
37
replies
7.5k
views
12 follow
Forum:
The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 3 months ago by
Ram
39k • written 9.8 years ago by
Niallhaslam
2.3k
29
votes
37
replies
2.6k
views
8 follow
Perl/Python script: phased vcf to phased tped
vcf
ped
phased
4.6 years ago by
Shicheng Guo
★ 9.3k
5
votes
37
replies
2.7k
views
search text in one file and then replace with text from another file
search
replace
multiple files
5.6 years ago by
mforthman
▴ 40
130
votes
37
replies
12k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 11.8 years ago by
Pals
★ 1.3k • written 11.8 years ago by
Sirus
▴ 820
1,000 results • Page
3 of 20
Recent Votes
Answer: How to sort gff3 according to chromosome order?
Answer: how to sort unique seq from fasta files
Answer: Make a BedGraph file
Answer: Finding Enhancers using Genomation library
A: Extracting N positions from fasta file
Comment: Gene enrichment analysis
Comment: Gene enrichment analysis
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Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file
by
kirillkirilenko
▴ 10
It works, thank you!
Comment: CNNScoreVariants Error
by
Pierre Lindenbaum
154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
Cathal
• 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
Answer: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
genomation is based on GenomicRanges which uses 1-based coordinates. https://www.biostars.org/p/84686/ Since a single CpG has a length o…
Comment: Gene enrichment analysis
by
ATpoint
72k
I cannot speak for this package but I recommend clusterProfiler where the universe argument isindeed all tested genes so your background.
Answer: Finding Enhancers using Genomation library
by
ATpoint
72k
You cannot derive enhancers from methylation profiles. Enhancers are regulatory elements, and they either are methylated or not. There is l…
Answer: convert data frame with character column to data frame with integer column
by
Basti
★ 1.5k
Cross-posted and answered there : https://stackoverflow.com/questions/76388032/convert-data-frame-with-character-column-to-data-frame-with-…
Comment: Getting same value for start and end position, "DNA methylation"
by
Basti
★ 1.5k
Your question lacks precision, we do not know what you are talking about
Comment: Gene enrichment analysis
by
Meisam
▴ 180
If you want to find enrichment of your selected genes versus the superset of all genes detected, then yes you mean the background. And to d…
Comment: WGCNA Trait File Issues
by
LChart
2.6k
The NAs are coming from the fact that each 'Sample' (which I assume is a unique identifier for a sample) is not actually a number and so th…
Answer: Why is coordinate sort required before findng read depths?
by
zhang yi xing
▴ 10
hi ,you can look at this fig in software **mosdepth** . By traversing a sorted BAM file from the beginning, one can obtain depth informat…
Comment: Getting species names and taxa id from assembly accession number
by
Mensur Dlakic
★ 23k
You should probably not advertise your personal email. It is not needed to understand the code. I don't know what exactly is the problem w…
Answer: how to sort unique seq from fasta files
by
shenwei356
8.1k
[seqkit common](https://bioinf.shenwei.me/seqkit/usage/#common) finds common sequences of multiple files by id/name/sequence seqkit co…
Answer: how to sort unique seq from fasta files
by
Mensur Dlakic
★ 23k
[**CD-HIT**][1] will remove all sequences that share identity above a certain threshold. If you set that threshold at `1.0` (meaning 100% i…
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