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108,024 results • Page
1 of 2161
Sort: Rank
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0
votes
0
replies
12
views
How to determine the optimal number of clusters?
clustering
clusters
35 minutes ago by
melissachua90
▴ 40
0
votes
0
replies
8
views
R bug during normalize
seurat
R
36 minutes ago by
Andy
▴ 20
0
votes
0
replies
9
views
Reference panel when doing ADMIXTURE
admixture
1 hour ago by
Karan
• 0
0
votes
1
reply
24
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL
structure
protein
1 hour ago by
spence.lank
▴ 10
0
votes
0
replies
13
views
Alternatives to ProtExcluder in repeat annotation/MAKER?
repeats
esl-fetch
annotation
ProtExcluder
MAKER
2 hours ago by
evoecogen
▴ 20
0
votes
6
replies
391
views
how to get an average ROC curve after 10-fold cross validation in r
r
cross-validation
curve
roc
2 hours ago by
Lisa
• 0
4
votes
11
replies
2.4k
views
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 1 hour ago by
Juke34
7.5k • written 2.8 years ago by
William
★ 5.1k
6
votes
2
replies
126
views
Seurat or Bioconductor for single cell RNA seq
single-cell
bioconductor
seurat
RNAseq
updated 4 hours ago by
Basti
★ 1.3k • written 5 hours ago by
Sandra
▴ 10
6
votes
3
replies
13k
views
fastq-dump split-spot and skip-technical
fastq-dump
split-spot
skip-technical
updated 5 hours ago by
Larissa Graciano
• 0 • written 7.0 years ago by
Shicheng Guo
★ 9.2k
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
Biostar
1.5k • written 6.2 years ago by
Istvan Albert
96k
0
votes
2
replies
91
views
Miseq mothur error with SOP in galaxy - Help please!
mothur
miseq
16s
Galaxy
sop
updated 3 hours ago by
colindaven
4.4k • written 6 hours ago by
Melissa
• 0
0
votes
2
replies
76
views
Find corresponding branch from gene tree in species tree
phylogeny
family-tree
gene
species
phylogenetics
1 hour ago by
Charlotte West
▴ 40
2
votes
3
replies
128
views
How to summarize the expression of a gene when having expression data from different transcripts of that gene
rnaseq
expression
updated 4 hours ago by
i.sudbery
16k • written 7 hours ago by
jeni
▴ 90
0
votes
2
replies
97
views
How can I creating multisample VCF file ?
VCF
updated 4 hours ago by
Ram
38k • written 7 hours ago by
eennadi
▴ 20
0
votes
0
replies
62
views
How to identify the batch informations from the sample ID?
batch-correction
TCGAbatch
DESeq2
TCGA
updated 4 hours ago by
Ram
38k • written 8 hours ago by
dare_devil
★ 1.7k
0
votes
1
reply
71
views
Adaptor sequences in GIAB samples
illumina
GIAB
adaptor
cutadapt
updated 7 hours ago by
GenoMax
125k • written 9 hours ago by
Mk
▴ 10
0
votes
1
reply
120
views
exchange the monocle data with Seurat
monocle3
Seurat
updated 9 hours ago by
fracarb8
▴ 890 • written 21 hours ago by
alghezim1
• 0
0
votes
6
replies
201
views
Differentially gene expression analysis
Limma
Deseq
R
updated 7 hours ago by
Victor J. Fernández
▴ 40 • written 11 hours ago by
Nai
▴ 20
0
votes
0
replies
76
views
News:
Introduction to GWAS course (6th edition) - June, 5th-8th
Bioinformatics
GWAS
R
11 hours ago by
carlopecoraro2
★ 2.2k
0
votes
2
replies
169
views
docker build Command Works Yet It Does Not Create A Docker Container
Linux
build
R
docker
2 hours ago by
Indira
• 0
0
votes
3
replies
102
views
pileup consolidation tool
RNAseq
pileup
jacusa
samtools
9 hours ago by
joe
▴ 380
0
votes
3
replies
152
views
Problem with tximport and plasmodium falciparum
tximport
updated 1 hour ago by
ATpoint
69k • written 16 hours ago by
bioinfo
▴ 20
0
votes
2
replies
150
views
How I know the genome assembly quality by the low coverage Pacbio data ?
genome
Pacbio
9 hours ago by
wdpang
• 0
3
votes
3
replies
143
views
How to map and annotate gene symbols to gene type?
Ensembl
RefSeq
UCSC
biomart
RNA-Seq
updated 15 hours ago by
GenoMax
125k • written 17 hours ago by
mohammedtoufiq91
▴ 170
0
votes
1
reply
80
views
Stringtie prepDE.py script
deseq2
stringtie
updated 1 hour ago by
Buffo
★ 2.0k • written 16 hours ago by
Aiswarya
• 0
1
vote
4
replies
161
views
BLAST reference genome indexing
blastn
fasta
shell
updated 4 hours ago by
GenoMax
125k • written 16 hours ago by
bhumm
▴ 20
0
votes
2
replies
126
views
Averaging across multiple proteomic experiments
statistics
proteomics
R
updated 4 hours ago by
ATpoint
69k • written 17 hours ago by
bhumm
▴ 20
0
votes
2
replies
149
views
Copy Number Variants, where to start?
CNV
annotation
3 hours ago by
paolo
▴ 60
6
votes
6
replies
302
views
command line - how to change name of multiple files at the same time
bash
line
command
script
updated 18 hours ago by
shenwei356
7.8k • written 1 day ago by
tiziana
• 0
0
votes
1
reply
1.3k
views
rDGIdb - VCF input error using locateVariant command (VariantAnnotation)
genome
sequence
updated 19 hours ago by
Gaurav
• 0 • written 3.2 years ago by
tarapcsakszabolcs
• 0
0
votes
0
replies
80
views
mosdepth coverage & transcripts per million
TPM
coverage
metagenome
mosdepth
19 hours ago by
hannahf
• 0
0
votes
2
replies
142
views
FATAL: While performing build: build image size <= 0 - Issues With Singularity
R
Docker
Singularity
5 hours ago by
Indira
• 0
0
votes
1
reply
108
views
Dealing with variable sequencing depth.
BCFTools
downsampling
WGS
sequencing
GATK
10 minutes ago by
a
• 0
0
votes
5
replies
300
views
Error: ##fileformat=VCFv4.2 does not exist
Pharmcat
VCF
updated 20 hours ago by
sbstevenlee
▴ 480 • written 2 days ago by
taniamahmood38
▴ 20
0
votes
1
reply
117
views
Extract species-specific SNPs from VCF files
SNPs
vcf
tools
updated 21 hours ago by
cfos4698
▴ 580 • written 22 hours ago by
RT
▴ 370
0
votes
0
replies
85
views
Questions about HVGs and HEGs in single cell research
single-cell
machine-learning
updated 20 hours ago by
Ram
38k • written 21 hours ago by
me
• 0
0
votes
0
replies
77
views
average expression function and pct
seurat
average
pct
expression
and
22 hours ago by
rasing02
• 0
0
votes
0
replies
85
views
GoSemSIm - function mgeneSim() is resulting in similarity matrix without 1s od diagonal
vs
Gosim
GoSemSIm
23 hours ago by
eliska.ochodkova
• 0
0
votes
2
replies
152
views
Database with gene family annotations
RNA-seq
database
23 hours ago by
kjs22
• 0
0
votes
2
replies
152
views
Error with FindConservedMarkers()
FindConservedMarkers
1 day ago by
Chris
▴ 60
2
votes
3
replies
224
views
comparing two metagenomics data sets
metagenomics
updated 1 day ago by
Mensur Dlakic
★ 22k • written 1 day ago by
arshad1292
▴ 80
1
vote
2
replies
140
views
Can't view the last rows
scRNA-Seq
updated 1 day ago by
brunobsouzaa
▴ 800 • written 1 day ago by
Chris
▴ 60
1
vote
4
replies
282
views
General approach for unsupervised clustering of bulk RNAseq samples and deriving/applying gene signature
clustering
RNAseq
DESeq2
11 hours ago by
Matthias
▴ 70
0
votes
0
replies
91
views
Extract different variants of a vcf file comparing to other vcf files
gatk
bedtools
mutect2
vcftools
variant
6 hours ago by
minoo
▴ 10
1
vote
2
replies
158
views
make BED file from existing BIM and FAM files
plink
updated 1 day ago by
chrchang523
10.0k • written 1 day ago by
josephine.henry
• 0
0
votes
3
replies
198
views
BWA-mem not working with Snakemake + singularity
snakemake
bwa
singularity
updated 1 day ago by
Jeremy Leipzig
21k • written 1 day ago by
brunobsouzaa
▴ 800
1
vote
2
replies
115
views
download a set of proteome from uniprot
uniprot
download
batch
6 hours ago by
Juke34
7.5k
1
vote
8
replies
1.8k
views
calctruequality in bbmap
Assembly
BBtools
calctruequality
q score
BBmap
updated 1 day ago by
Andreas
★ 2.5k • written 4.8 years ago by
coyk
• 0
0
votes
2
replies
182
views
Tool to combine Germline Variant call from different variant callers
haplotypecaller
gatk
snps
9 hours ago by
rohitsatyam102
▴ 690
6
votes
4
replies
156
views
Equivalent to SeqMan alignment tool
SeqMan
alignments
1 day ago by
A_heath
▴ 120
108,024 results • Page
1 of 2161
Recent Votes
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date
Comment: Subbmission Data
Comment: Subbmission Data
Answer: Subbmission Data
Answer: how I can install lumi, plier, simpleaffy, oligo classes, LMGene and siggens pac
Comment: Bacterial metatranscriptomics with DESEQ2?
C: How to extend contigs from single-end reads?
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Recent Awards •
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Popular Question
to
epaminonda
▴ 10
Popular Question
to
Elisabeth Gasteiger
★ 2.2k
Popular Question
to
mathavanbioinfo
▴ 70
Popular Question
to
cgds
▴ 10
Teacher
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Basti
★ 1.3k
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7.8k
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GenoMax
125k
Recent Replies
Comment: Subbmission Data
by
seidel
10k
GEO allows you to keep your data private for up to three years, AND has a mechanism where you can share it with reviewers without it being …
Comment: PyMOL: Gaps in protein structure yet shown by the sequence
by
spence.lank
▴ 10
The PDB ID for this structure is 7DK3 and the literature is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775788/
Comment: Problem with tximport and plasmodium falciparum
by
ATpoint
69k
You do not do what I suggested above.
Comment: Relative frequencies of the nucleotides in Fasta files
by
xiaoleiusc
▴ 110
Hi, Hugo, I acknowledged you in my paper recently published. Thanks for your help! Xiao PS, paper link https://elifesciences.org/articles/8…
Comment: Stringtie prepDE.py script
by
Buffo
★ 2.0k
from the manual: -i a folder containing all sample sub-directories, or a text file with sample ID and path to its GTF file on each lin…
Comment: Using Entrez Utilities to query the Nucleotide database by collection_date
by
anomalous.lexeme
• 0
That looks pretty useful. I'll give that a try as well. Thank you very kindly for the help.
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Juke34
7.5k
This script does not exist anymore in recent releases. Without any example I cannot help.
Comment: Create de novo repeat library
by
evoecogen
▴ 20
Are there any alternatives to ProtExcluder? I suddenly started to have problems with v1.2: The files blastx.out.fnolowm50seqm and blastx.o…
Comment: Find corresponding branch from gene tree in species tree
by
Charlotte West
▴ 40
Following your suggestion I've been playing around with Notung and seems like its got a lot of great features. I ran: ``` java -jar notung …
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Lisa
• 0
thanks for your help
Comment: docker build Command Works Yet It Does Not Create A Docker Container
by
Indira
• 0
So - I am trying to get around proxy issues but essentially installing required packages in a docker/sif then trying to use that to run an …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Ram
38k
Do not add answers unless you're **answering** the top level question. Use `Add Comment` or `Add Reply` instead as appropriate. I've moved …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
BioinfoBee
• 0
@juke34 I tried the agat_sp_gxf_to_gff3.pl to sort the gff3 by their chromosome order but doesn't seems to work. Any suggestions?.
Comment: CNV Prediction Tools
by
Quentin M
▴ 60
Give a try to [CODEX2][1] [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y
Comment: Problem with tximport and plasmodium falciparum
by
bioinfo
▴ 20
Thank you. It does not seem to be that. I changed my script a bit. Now it looks like shown below: mart <- biomaRt::useMart("protists_…
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