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1,000 results • Page
1 of 20
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0
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1
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Suggestion for approaching multiple conditions scRNA-seq
scRNA-seq
1 minute ago by
Eisuan
▴ 20
0
votes
1
reply
28
views
Dealing with very large gene-lists in GSEA
R
fgsea
GSEA
updated 8 minutes ago by
Trivas
▴ 710 • written 1 hour ago by
yura.grabovska
▴ 50
0
votes
0
replies
11
views
i need to update MitoZ 3.4 to 3.5
mit0Z
assembly
tool
1 hour ago by
manaswiniparija3
▴ 10
0
votes
2
replies
247
views
Which GPU for local Colabfold
GPU
Alphafold
updated 1 hour ago by
matt_arnold_bio
• 0 • written 4 months ago by
Arjen Ten Have
▴ 360
0
votes
1
reply
52
views
boxplot issue
Boxplot
DESeq2
1 hour ago by
kalyani
• 0
0
votes
1
reply
43
views
heatmap issue
heatmap
DESeq2
updated 2 hours ago by
yura.grabovska
▴ 50 • written 2 hours ago by
kalyani
• 0
730
votes
161
replies
108k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 14 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
97k
3
votes
4
replies
274
views
differential gene analysis
DGE
2 hours ago by
kalyani
• 0
2
votes
2
replies
64
views
STAR solo set parameters for scrna-seq
solo
STAR
1 hour ago by
t.ru
▴ 20
1
vote
3
replies
72
views
merge vcf.gz file
vcf.gz
bcftools
1 hour ago by
Mali
• 0
0
votes
2
replies
80
views
GO enrichment analysis
enrichment
analysis
GO
2 hours ago by
hellokwmin
• 0
6
votes
6
replies
2.4k
views
Sites for Computer Aided Drug Designing
CADD
Simulations
in-silico
Docking
updated 3 hours ago by
contact
• 0 • written 8.2 years ago by
ruchikabhat31
▴ 60
0
votes
3
replies
620
views
database on patients treated with CAR T-cell therapies
cancer
updated 3 hours ago by
contact
• 0 • written 16 months ago by
yueli7
▴ 240
0
votes
1
reply
72
views
installation of Snapgene tool in Ubuntu
installation
snapgene
Ubuntu
updated 4 hours ago by
ATpoint
70k • written 4 hours ago by
Fizzah
▴ 20
1
vote
3
replies
111
views
mpileup to sync file
AF
samtools
selection
vcf
popoolation
updated 3 hours ago by
Pierre Lindenbaum
153k • written 4 hours ago by
qstefano
▴ 20
0
votes
0
replies
59
views
Quality control of Chip-seq data (NRF and PCB)
control
library
quality
PCB
Chip-seq
NRF
4 hours ago by
michelafrancesconi9
• 0
0
votes
1
reply
165
views
Variant caller reports a homozygous variant genotype, but more reads are associated with reference
bcftools
variants
updated 4 hours ago by
colindaven
4.6k • written 1 day ago by
rebeliscu
▴ 50
0
votes
0
replies
52
views
News:
Cellosaurus release 45 is available
knowledgebase
news
cell
line
5 hours ago by
Amos Bairoch
▴ 110
0
votes
2
replies
2.5k
views
demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_strand_adapter --detect_mid_strand_barcodes produce > 90% of unclassified …
demultiplexing
guppy
just now by
andres.firrincieli
3.1k
0
votes
1
reply
87
views
Snakemake doesn't recognize output files even though they are created
python
Snakemake
updated 4 hours ago by
Shred
★ 1.0k • written 6 hours ago by
DdogBoss
• 0
0
votes
0
replies
53
views
GO analysis using diamond blastp output
blastp
GO
analysis
Diamond
6 hours ago by
hellokwmin
• 0
8
votes
10
replies
530
views
7 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming
Masters
updated 9 hours ago by
cfos4698
▴ 720 • written 8 days ago by
rackbersingh
• 0
0
votes
0
replies
61
views
Diffbind: how to get raw read counts and normalized read counts
Diffbind
rawcount
9 hours ago by
soda
▴ 40
0
votes
1
reply
83
views
Is it possible to use pseudoalignments.bam to run rMATs?
Kallisto
rMATs
updated 10 hours ago by
dsull
★ 4.0k • written 11 hours ago by
Lillian
• 0
0
votes
1
reply
79
views
Total No of Genes of GENCODE Release 43
gene
numbers
updated 2 hours ago by
ATpoint
70k • written 11 hours ago by
ahmad
• 0
1
vote
1
reply
107
views
When to merge multiple fastq files into one for RNAseq analysis?
rnaseq
aligning
bowtie2
updated 12 hours ago by
GenoMax
127k • written 12 hours ago by
lunarskye222
• 0
0
votes
2
replies
106
views
genome annotation [sstart] [send] - how to get protein sequence from gene
genome
annotation
2 hours ago by
danfarkas
• 0
0
votes
0
replies
68
views
Error at phase 4 when running GeMoMa (homology-based annotation)
Homology
GeMoMa
Annotation
Genome
14 hours ago by
breannar
• 0
0
votes
0
replies
79
views
Passing strings for password, email authentication and download link
bash
datasets
curl
download
offtopic
updated 4 hours ago by
ATpoint
70k • written 15 hours ago by
pr2009
▴ 10
12
votes
9
replies
683
views
6 follow
How to find promoter sequence of a gene?
promoter
17 hours ago by
sunyeping
▴ 80
1
vote
4
replies
198
views
bash command to process a line
linux
command
updated 16 hours ago by
GenoMax
127k • written 17 hours ago by
saadleeshehreen
▴ 110
0
votes
0
replies
65
views
News:
Virtual RAD-seq Analysis Workshop!
workshops
popgen
genomics
rad-seq
18 hours ago by
mia.nahom
▴ 10
1
vote
4
replies
166
views
Centromere and telomere positions for Chm13v2 assembly
centromere
chm13v2
18 hours ago by
arsala521
▴ 10
0
votes
5
replies
232
views
featureCounts problem in reading Gff
featureCounts
GFF
RNA-seq
updated 16 hours ago by
Ram
38k • written 19 hours ago by
Beatrice
• 0
4
votes
0
replies
69
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
updated 18 hours ago by
Ram
38k • written 20 hours ago by
Wubin
▴ 40
2
votes
2
replies
130
views
Retrieve hgnc_symbol from XM_ refseqs using BiomaRt
refseq_mrna_predicted
biomaRt
refseq
XM
5 hours ago by
ladina.hoesli
• 0
0
votes
1
reply
111
views
Time change in expression vs time change in phenotype
RNA-Seq
DGE
DESeq2
10 hours ago by
Ivan
• 0
0
votes
0
replies
66
views
How to perform a gsva assessing for the directonality of the genes.
gsva
21 hours ago by
roybatty269
• 0
0
votes
4
replies
897
views
activity of unloaded/unassembled Tn5
sequencing
next-gen
updated 21 hours ago by
ATpoint
70k • written 5.1 years ago by
zhaohainancau
• 0
7
votes
7
replies
484
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 20 hours ago by
Ram
38k • written 22 hours ago by
Raygozak
★ 1.4k
3
votes
6
replies
397
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
updated 20 hours ago by
jv
★ 1.0k • written 7 days ago by
Sian
▴ 20
0
votes
1
reply
77
views
syntax errors when running part3 all-against-all
error
AssertDatabaseVersionsInSync
syntax
all-against-all
updated 22 hours ago by
Ram
38k • written 22 hours ago by
Sofia
• 0
1
vote
0
replies
95
views
Herald:
The Biostar Herald for Tuesday, March 28, 2023
herald
23 hours ago by
Biostar
1.6k
1
vote
4
replies
452
views
Retrieve protein sequence from Mgnify given only accession code
Mgnify
API
updated 23 hours ago by
biomarco
▴ 20 • written 9 months ago by
jscience
• 0
1
vote
1
reply
195
views
Browsing MGnify IDs and clusters
metagenomics
mgnify
ebi
23 hours ago by
biomarco
▴ 20
0
votes
0
replies
70
views
calculation of calibration factors using impuation reference panel and ethnicity
GWAS
Calibration
factor
1 day ago by
parveenkayenat
• 0
1
vote
4
replies
194
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
2 hours ago by
Agamemnon
▴ 60
0
votes
0
replies
74
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftool
1 day ago by
Nai
▴ 50
6
votes
1
reply
161
views
what is IGV visualization lighter color variants stand for
visualization
vcf
IGV
updated 1 day ago by
Jorge Amigo
14k • written 1 day ago by
zhangfish
▴ 50
0
votes
2
replies
1.6k
views
Error when changing the database for minfi dropLociWithSnps
SNP
minfi
methylationEPIC
illumina
methylation
updated 1 day ago by
Satu
• 0 • written 5.7 years ago by
Ellen O
▴ 20
1,000 results • Page
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Recent Votes
PyComplexHeatmap: a Python package to visualize multimodal genomics data
pulling snps from vcf file using ids
A: pulling snps from vcf file using ids
Answer: Scaling RNA-Seq data before clustering?
Answer: How to use CAFE from Orthofinder Results
Answer: merge vcf.gz file
STAR solo set parameters for scrna-seq
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Answer: Dealing with very large gene-lists in GSEA
by
Trivas
▴ 710
IMO, in those cases you could look at ES instead of NES. Regardless, within the function `fgsea`, you can set the parameters `minSize` and …
Comment: merge vcf.gz file
by
Mali
• 0
file1 = '/sci/labs/orzuk/orzuk/projects/Skin/data/Ichilov/vcfFiles/vcfFiles/eb3_1001_748-gatk-haplotype.final.vcf.gz' file2 = '/sci/labs/or…
Comment: Which GPU for local Colabfold
by
matt_arnold_bio
• 0
Another giveaway is that when you hit run, it will say either "Running on GPU" or "Running on CPU" in the log output... ![enter image desc…
Answer: Which GPU for local Colabfold
by
matt_arnold_bio
• 0
Hi Arjen, This is a little while ago now so maybe this is not that helpful but... You should be able to tell if the GPU is being seen…
Comment: STAR solo set parameters for scrna-seq
by
t.ru
▴ 20
it's single cell mars-seq. Yes sorry its a fastq file.
Answer: boxplot issue
by
yura.grabovska
▴ 50
First of all, you're not outputting the result of your scale to anything... t(apply(mat, 1, scale)) colnames(mat) <- rownames(cold…
Comment: STAR solo set parameters for scrna-seq
by
GenoMax
127k
> a fasta file similar to this This is not a fasta file It is a fastq format file. Are you sure this is single cell RNAseq data? Looking…
Answer: heatmap issue
by
yura.grabovska
▴ 50
Your controls clearly show variable expression for the genes you're plotting so to get them to stick together on the left, you would need t…
Comment: How to demultiplex single end - dual index run - NextSeq 500
by
GenoMax
127k
Correct. This is a single-end dual indexed (8 bp each) run.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene
by
danfarkas
• 0
Hi shenwei356, Thanks for the clarification. However, I did try this, and it was not yielding the expected amino acid sequences. This is w…
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on
by
Agamemnon
▴ 60
I ran ```samtools view -F 4 -q 42 test.bam | wc -l``` and I get ```6159141```, why is there a discrepancy, as originally only ```5200484```…
Comment: differential gene analysis
by
kalyani
• 0
okay thankks!
Comment: Kallisto bustools for scRNA-seq
by
t.ru
▴ 20
@SRR17050039.1 NB501465:544:HF2H7BGXB:1:22104:14442:1233_TCCTGAGC_barcode=NA-EEEE-AAAAAEE-EEEEEEEE-GCTG-TGCCAGA-ACGTTCAT-W202012/1 GCCCTGTA…
Comment: merge vcf.gz file
by
Pierre Lindenbaum
153k
"file 1 " , with a space, cannot be a real argument. show us the real filenames please, and the error messages.
Answer: merge vcf.gz file
by
ATpoint
70k
You must compress with bgzip. gzip -d your.vcf.gz bgzip your.vcf
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