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117,115 results • Page
1 of 2343
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0
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0
replies
5
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Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
subset
10 minutes ago by
sc_analysis
• 0
0
votes
0
replies
5
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
8 minutes ago by
bio_info
▴ 10
2
votes
3
replies
312
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
10 minutes ago by
txema.heredia
▴ 130
0
votes
0
replies
21
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
36 minutes ago by
doramora
▴ 10
0
votes
0
replies
19
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
1 hour ago by
Emily
▴ 20
2
votes
3
replies
113
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
1 hour ago by
hashim.rana11
▴ 20
0
votes
1
reply
75
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 2 hours ago by
Pierre Lindenbaum
162k • written 4 hours ago by
Maksim
• 0
0
votes
1
reply
75
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
updated 2 hours ago by
zx8754
11k • written 8 hours ago by
F110152169
• 0
800
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
8
votes
9
replies
3.0k
views
7 follow
Venter Genome Vcf
vcf
updated 9 hours ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
0
votes
9
replies
531
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 2 hours ago by
zx8754
11k • written 6 days ago by
hannes.bongartz
• 0
0
votes
0
replies
68
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 12 hours ago by
Ram
44k • written 13 hours ago by
Christopher
▴ 10
4
votes
1
reply
135
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 13 hours ago by
swbarnes2
14k • written 18 hours ago by
May Ling
• 0
0
votes
0
replies
54
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 13 hours ago by
GenoMax
142k • written 13 hours ago by
jway
• 0
0
votes
3
replies
215
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 11 hours ago by
ATpoint
82k • written 14 hours ago by
shahzaibali
• 0
0
votes
1
reply
116
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 14 hours ago by
jared.andrews07
★ 17k • written 18 hours ago by
atan
• 0
0
votes
2
replies
159
views
What do the transcript variant # mean in RefSeq?
refseq
updated 14 hours ago by
Ram
44k • written 17 hours ago by
curious
▴ 750
4
votes
6
replies
329
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
14 hours ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
226
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 13 hours ago by
Jeremy
▴ 910 • written 1 day ago by
Mohamed Samir
▴ 30
2
votes
0
replies
111
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
18 hours ago by
Matthias Zepper
4.6k
0
votes
1
reply
89
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 18 hours ago by
Ram
44k • written 18 hours ago by
a.bibek52
▴ 10
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 18 hours ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
101
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
2 hours ago by
mtabaka
• 0
0
votes
1
reply
95
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 18 hours ago by
Papyrus
★ 2.9k • written 19 hours ago by
June
• 0
0
votes
2
replies
616
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 19 hours ago by
June
• 0 • written 10 months ago by
rkb965
• 0
2
votes
5
replies
236
views
Z score
Z-score
updated 19 hours ago by
Ram
44k • written 1 day ago by
Akash D
▴ 60
2
votes
6
replies
245
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
2 hours ago by
bio_info
▴ 10
3
votes
3
replies
157
views
Unexpected read length from NGS
NGS
Illumina
1 hour ago by
QX
• 0
0
votes
1
reply
105
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 4 hours ago by
cmdcolin
★ 3.8k • written 22 hours ago by
adarsh_pp
▴ 40
1
vote
6
replies
287
views
samtools write-index
samtools
updated 22 hours ago by
aw7
▴ 310 • written 2 days ago by
LucisTheFather
• 0
0
votes
2
replies
209
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 23 hours ago by
i.sudbery
19k • written 2 days ago by
Varsha
• 0
3
votes
2
replies
142
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
egascon
• 0
0
votes
0
replies
69
views
GWAS or QTL mapping in RIL population
GWAS
RIL
1 day ago by
韩雨
• 0
0
votes
0
replies
74
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 19 hours ago by
Ram
44k • written 1 day ago by
emmanouil.a
▴ 120
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 18 hours ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
249
views
GWAS Phenotypes
GWAS
updated 1 day ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.1k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 1 day ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
1
vote
1
reply
117
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
azeu
▴ 10
0
votes
0
replies
56
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
1 day ago by
Linus
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 1 day ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
131
views
Free AI for R programming
R
updated 19 hours ago by
Ram
44k • written 1 day ago by
mohamadzare6022
▴ 10
7
votes
13
replies
805
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 19 hours ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
0
votes
0
replies
90
views
Extracting haplotype-specific annotations from splicing graph
vg
1 day ago by
Juhyun
• 0
0
votes
0
replies
84
views
miloR - object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance
scRNA-seq
seurat
miloR
1 day ago by
shuaizh117
▴ 10
0
votes
0
replies
87
views
Phyloseq returning black bars for plot_bar
phyloseq
bioconductor
R
1 day ago by
Jacob
• 0
3
votes
8
replies
867
views
Random Access remote BAM files
htslib
BAM
updated 1 day ago by
a.penatauber
• 0 • written 3 months ago by
Lucas R.F.
▴ 20
0
votes
0
replies
93
views
Cancer vs Normal Cell Classification Based on SNVs
cancer
1 day ago by
dglad
• 0
0
votes
4
replies
207
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
1 day ago by
reza
▴ 300
0
votes
1
reply
122
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 19 hours ago by
Ram
44k • written 1 day ago by
avelarbio46
▴ 30
0
votes
1
reply
135
views
Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
RNAseq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Fossil
• 0
117,115 results • Page
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Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
Update: I ran CellBender on these samples and compared its results with SoupX and DecontX. vs SoupX: ![cellbender vs SoupX][1] …
Comment: Unexpected read length from NGS
by
QX
• 0
thank you all!
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
by
hashim.rana11
▴ 20
Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity![nucleoti…
Comment: Best Practice On Variant Discovery For Bacteria?
by
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I used HaploTypecaller but my plasmid reads are not present in the output vcf file ... but it's there in my input file
Answer: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
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Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1] Then, pi, Tajima's D, and oth…
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I used `seqkit split` to divide the query FASTA file into 10 parts and then ran `diamond blastp` on each file using 44 threads. The process…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
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zx8754
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Try: `--covar-name SEX,PARKISON` FID and IID are Family ID and Individual ID, they are not covariates. Side note, if PARKISON means "Par…
Comment: Error with BiocParallel. No barcodes files found
by
bio_info
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I understand, thanks for explaining this to me. I'll take care of this in future.
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool
by
Pierre Lindenbaum
162k
> , but I was unsuccessful. what does it mean ?
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Prokka works the same on both forward and reverse complementary reads. It doesn't matter if your genetic sequences are in their original fo…
Comment: Construction of circos plot from WGS data
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Anitha
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Thank you for the information. But, I am still struggling like which data to use and how to process the input data to represent to build th…
Comment: Tools for chromosomal aneuploidy detection
by
cmdcolin
★ 3.8k
is there any reason why you do not like tools based on read depths?
Comment: CreateSeuratObject taking very long
by
eae6d2e7
• 0
Thank you for your reply! I followed your advice to convert to sparse matrix first but I got this error Error in Matrix::sparseMatrix(raw_…
Answer: Venter Genome Vcf
by
ericrkofman
▴ 20
I can't find an hg38 version, and the old VCF seems to be of a different header format so I am having difficulty converting it to hg38 from…
Comment: What is a good way to do gene differentials in single cell data where one group
by
ATpoint
82k
Preferred if you have true biological replicates. Can still be combined with my subsetting strategy, like use 100x different cells for the …
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