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1,000 results • Page
3 of 20
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0
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125
views
News:
Announcing workshop on Declarative Programming in Biology and Medicine (Seattle, Sept. 2023)
medicine
declmed
declarative
icfp
precision
4 days ago by
Stephen
• 0
1
vote
1
reply
146
views
How to generate GFF/GTF file from cDNA transcipts FASTA file?
gff3
gtf
transcript
cDNA
updated 4 days ago by
Pierre Lindenbaum
153k • written 4 days ago by
BioinfoBee
• 0
0
votes
0
replies
131
views
BULK mRNA-seq with UMIs. Does it make sense to run bedtools genomecov?
RNAseq
gene-length
normalization
4 days ago by
txema.heredia
▴ 70
1
vote
3
replies
289
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
updated 4 days ago by
jv
★ 1.0k • written 6 days ago by
Sian
• 0
0
votes
0
replies
118
views
Browsing MGnify IDs and clusters
metagenomics
mgnify
ebi
4 days ago by
biomarco
▴ 20
0
votes
0
replies
121
views
Deeptools clustering differs when clustering sample as standalone and together with other samples
deepTools
4 days ago by
jordi.planells
▴ 450
2
votes
5
replies
293
views
ExomeDepth installation error
ExomeDepth
Exome
CNV
updated 4 days ago by
jared.andrews07
★ 14k • written 4 days ago by
Medha
• 0
2
votes
6
replies
315
views
bioinformatics problems solved by graphs data structure
Graph
algorithm
data-structure
updated 4 days ago by
Ram
38k • written 4 days ago by
abdelmalek.benmeziane
• 0
2
votes
3
replies
176
views
Reduce poly-N regions longer than 200bp back to 200bp in a reference genome FASTA
FASTA
poly-N
4 days ago by
William
★ 5.2k
0
votes
1
reply
137
views
Embedded stop codon in translated nucleotide sequences in DAMBE
DAMBE
stop-codon
updated 4 days ago by
Mensur Dlakic
★ 23k • written 4 days ago by
Fathima
• 0
3
votes
5
replies
363
views
PCA in gene expression
PCA
TCGA
3 days ago by
ali
• 0
2
votes
1
reply
286
views
How to derive conditional maximum likelihood of the sum of independent negative binomial variables?
limma
voom
biostatistics
4 days ago by
Dan
▴ 90
3
votes
3
replies
197
views
What means this Error when running a script in python??
python3
yaml
conda
linux
python
updated 4 days ago by
Ram
38k • written 4 days ago by
Ant
• 0
4
votes
3
replies
290
views
Informations for gene summary are missing in eutils api of NCBI?
NCBI
esummary
eutils
Gene
updated 4 days ago by
MirianT_NCBI
▴ 460 • written 4 days ago by
dare_devil
★ 1.7k
0
votes
1
reply
149
views
ImportError: Bio.Alphabet has been removed from Biopython
Biopython
updated 4 days ago by
Wayne
★ 1.7k • written 4 days ago by
Neel
▴ 10
4
votes
4
replies
202
views
Differences between BioMart and Ensembl site
ensembl
biomart
transcripts
refseq
4 days ago by
jpuntomarcos
▴ 50
0
votes
1
reply
278
views
Sequence statistics to report viruses (or bacteria and fungi) using Nanopore for diagnostic purpose
nanopore
updated 4 days ago by
colindaven
4.6k • written 20 days ago by
pixie@bioinfo
★ 1.5k
0
votes
0
replies
112
views
Can't initialise orthomcl schema at orthomclInstallschema step.
mysql
perl
orthomcl
4 days ago by
shivankparashar
• 0
0
votes
1
reply
160
views
Clinvar Mapping
gene
Clinvar
Mapping
updated 4 days ago by
Pierre Lindenbaum
153k • written 4 days ago by
Shweta
• 0
3
votes
2
replies
214
views
correlations in R
cor
R
4 days ago by
rene.j.erhardt
▴ 20
0
votes
1
reply
747
views
Astalavista landscape AS gtf file output
rna-seq
Astalavista
updated 5 days ago by
xizengde
• 0 • written 4.7 years ago by
dina.hesham139
▴ 160
1
vote
2
replies
219
views
Weird looking dispersion & MA plot?
deseq2
RNA-seq
updated 4 days ago by
Ram
38k • written 5 days ago by
Neha
• 0
3
votes
8
replies
2.9k
views
8 follow
Using AWS for Bioinformatics
unix
Cluster
updated 4 days ago by
4galaxy77
2.6k • written 17 months ago by
dk0319
▴ 40
1
vote
2
replies
181
views
Stringtie does not work with NCBI GTF file?
Stringtie
DGE
updated 5 days ago by
Mensur Dlakic
★ 23k • written 5 days ago by
100dustedclays
▴ 10
0
votes
4
replies
1.7k
views
Bioinformatics Server on AWS
AWS
updated 4 days ago by
Ram
38k • written 3.1 years ago by
jyp327
• 0
2
votes
4
replies
242
views
Error with a function in ATAC-seq analysis
ATAC-seq
4 days ago by
Chris
▴ 70
2
votes
2
replies
214
views
Tool:
NCBI's Foreign Contamination Screen (FCS) tool improves the quality of GenBank submissions
NCBI
Submission
GenBank
3 days ago by
PeterC_NCBI
▴ 210
0
votes
0
replies
118
views
how to get genomic range for hi-c datasets in hdf5 file
R
hi-c
contact-map
genomic-ranges
updated 4 days ago by
Ram
38k • written 5 days ago by
rheab1230
▴ 140
0
votes
0
replies
127
views
Samtools: remove unmapped reads as well as reads that are mapped incorrectly
samtools
updated 5 days ago by
Ram
38k • written 5 days ago by
npavliukovec
• 0
1
vote
4
replies
608
views
"Error parsing strand (?) from GFF line" happenning in gffread, stringtie and cufflinks
cufflinks
gff
gffread
stringtie
updated 5 days ago by
hafiz.talhamalik
▴ 350 • written 8 weeks ago by
Guilherme
• 0
0
votes
0
replies
104
views
how to interpret hi-c heatmap hdf5 file
heatmap
maps
hdf5
hi-c
5 days ago by
rheab1230
▴ 140
1
vote
3
replies
301
views
Alignment REST API
emboss
rest-api
alignment
needle
python
updated 4 days ago by
Shred
★ 1.0k • written 5 days ago by
joselu
▴ 110
2
votes
12
replies
535
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 3 days ago by
Ram
38k • written 5 days ago by
Human
• 0
0
votes
0
replies
104
views
Gain of function amplifications - CCLE/cBioPortal
copy
gains
amplification
number
cBioPortal
CCLE
5 days ago by
Lakshmi
▴ 10
1
vote
0
replies
165
views
Tutorial:
ChIP-Seq Analysis Tutorial
Epigenetics
Bowtie2
MACS2
ChIP-Seq
Motif
updated 5 days ago by
ATpoint
70k • written 5 days ago by
Simon
▴ 20
0
votes
0
replies
101
views
Biomark Fluidigm delta delta CT method calculation
Fluidigm
Biomark
qPCR
5 days ago by
jms2520
▴ 20
100
votes
36
replies
27k
views
33 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 5 days ago by
Simon
▴ 20 • written 9.4 years ago by
14134125465346445
★ 3.6k
0
votes
0
replies
92
views
News:
Course live online Introduction to Bayesian Analyses using R, May 8th-12th, 2023
bayesian
RProject
course
online
5 days ago by
Sole
• 0
0
votes
0
replies
93
views
pyscenic cannot mapped to the feather file
pyscenic
5 days ago by
Andy
▴ 30
0
votes
0
replies
85
views
How to calculate Summary.csv statistics after re-running STARSolo cell filtering?
scRNA-seq
STARSolo
STAR
5 days ago by
ayeTown
• 0
0
votes
0
replies
97
views
Solving set of equations possibly with Matlab for affinity measurement with ELISA
set
ELISA
affinity
Matlab
equation
5 days ago by
field654
▴ 30
1
vote
2
replies
202
views
Multiple samples and species with kallisto bus(tools)
kallisto
scrnaseq
bustools
4 days ago by
tritone_858
• 0
0
votes
0
replies
99
views
how to get the nucleotide squence behind a symbolic ALT in VCF
SV
vcf
sniffles
3 days ago by
Maxine
• 0
0
votes
0
replies
154
views
How can I retrive the actual amino acid and the alternative amino acid (if any cordon changes happened due to editing)?
RNA
editing
5 days ago by
Genetics
▴ 20
0
votes
0
replies
89
views
pyscenic feather file
pyscenic
5 days ago by
Andy
▴ 30
1
vote
1
reply
150
views
Is there a site that takes a list of uniprot IDs/gene IDs as input and create radial phylogenetic tree?
phylogenetictree
5 days ago by
Diwan
▴ 650
0
votes
0
replies
85
views
Something wrong with my code concerning bsseq visualization
bsseq
plotRegion
R
5 days ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
94
views
How to bifurcate patients into high and low expressing groups for TCGA survival analysis for a gene of interest
Meidan
TCGA
Percentile
Survival
R
5 days ago by
Manav
• 0
0
votes
1
reply
172
views
Job:
Molecular biologist / clinical pharmacologist (f/m/d)
molecular
pharma
phamacology
biotech
biology
updated 4 hours ago by
Jeremy
▴ 770 • written 5 days ago by
D4office
• 0
0
votes
4
replies
266
views
Does it possible to know what are the adjacent genes up to 1000bp upstream and downstream of IS element
Transposons
4 days ago by
Neel
▴ 10
1,000 results • Page
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Recent Votes
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
smoothing or binning bigWig file
List of Ongoing and Planned Long Read Sequencing studies?
Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Answer: Read lengths greater than insert length
A: Changing Output From Gene ID to Symbol When Running findMarkers from Scran
Answer: BLAST Database error: No alias or index file found for nucleotide database
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Recent Replies
Comment: split fasta file to train deep learning model
by
shenwei356
7.9k
Excluding sequences containing any letter not belonging to the 20 [amino acids letters](https://github.com/shenwei356/bio/blob/master/seq/a…
Comment: split fasta file to train deep learning model
by
pinheirofabiano
▴ 10
@shenwei356, thank you very much for your help, perfect! But now I realized that some fasta sequences contain the letter "B", which is ou…
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
by
Mensur Dlakic
★ 23k
I think it depends on the speed of your local disks and the memory amount. On a single node, breaking up the database doesn't sound like a …
Comment: Sample size for population genetics
by
Jeremy Leipzig
21k
Other populations just make the model harder to generalize, not easier.
Comment: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
by
Vincent Laufer
★ 2.5k
i think there is some of that - my most upvoted comment of all time was a dismissive comment i made while extremely tired. for context i ha…
Comment: Molecular biologist / clinical pharmacologist (f/m/d)
by
Jeremy
▴ 770
Is this job on site in Vienna or remote?
Comment: smoothing or binning bigWig file
by
rls_08
▴ 40
if you use bigwigCompare , that would not create a sliding window, but instead, it will output the mean for each bin, according to the -bin…
Comment: Sample size for population genetics
by
zimmer.schweiz
• 0
Thank you so much for your answer. For common polygenic diseases, would it make sense to increase the number of populations sampled, in ord…
Answer: Sample size for population genetics
by
Jeremy Leipzig
21k
For a rare penetrant monogenic disease? A few cases. For a common polygenic disease or trait? 500k-10M
Answer: using GRanges metadata to constrain overlap searches between objects
by
seidel
11k
Rather than do all overlaps all the time for all samples, why not restrict the data by sample when you can. The code below works about 4 ti…
Comment: How to get gene from PSIBLAST resuts
by
Tom
• 0
Hello, thank you for your answer, I have a question, Why the information from the GFF file and from the feature table is different? I see …
Comment: SNP ID (rsID) to Chr no. and Position
by
Jewahir
• 0
Yeah, thank you for that!!
Comment: 1000 genomes hg38 with dbSNP rsid
by
Ram
38k
It should be pretty straightforward. Just to save you some pain, run these on the 1000g VCF once you download it: 1. `vt decompose -s` to …
Comment: 1000 genomes hg38 with dbSNP rsid
by
Vince
▴ 150
Yeah, I had some hope that I wouldn't need to mess with doing this ...
Answer: counting the unmapped reads
by
chemkhi.ali13
• 0
> Hi all, > > I have a sam file, my supervisor asked me to count the number of > unmapped reads, which command I should use? > > sam…
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