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55 results • Page
1 of 2
Sort: Views
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Views
Votes
Replies
0
votes
5
replies
2.8k
views
Graph using corrplot for multiple sets of data
R
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
rvsaras86
• 0
0
votes
0
replies
2.7k
views
CNV analysis from SNP6.0 data using Affymetrix power tools
cnv
apt-copynumber
SNP
affymetrix
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
cafelumiere12
▴ 80
0
votes
0
replies
2.2k
views
Coverage and Read Depth Recommendations by Sequencing Application
coverage
sequencing-depth
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
support
▴ 640
0
votes
5
replies
2.2k
views
CEGMA on human assembly
CEGMA
Assembly
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
ulike
• 0
0
votes
1
reply
2.2k
views
missing probeID in affymetrix using oligo package
affymetrix
updated 14 hours ago by
Ram
37k • written 7.7 years ago by
benhrif.oussama
• 0
1
vote
6
replies
2.0k
views
Error using samtools for downloading bam files
bam
samtools
updated 14 hours ago by
Ram
37k • written 7.7 years ago by
Maria333
▴ 20
0
votes
1
reply
1.8k
views
Comparison of two structures based on only partial similarly (comparison of cores of proteins/rna)
protein
structural-comparison
rna
updated 13 hours ago by
Ram
37k • written 7.8 years ago by
mmagnus
▴ 150
7
votes
8
replies
1.6k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 11 hours ago by
Ram
37k • written 7.7 years ago by
xiaofeng.dong12
▴ 20
0
votes
1
reply
1.4k
views
issues in genotyping using TaqMan Assay
TaqMan
genotyping
updated 12 hours ago by
Ram
37k • written 7.7 years ago by
jfjiang
▴ 10
0
votes
0
replies
1.4k
views
Using GWAS data to reproduce the gene candidate results
snp
updated 13 hours ago by
Ram
37k • written 7.7 years ago by
huudaudi
• 0
7
votes
4
replies
1.3k
views
microarray gene datasets
gene
updated 15 hours ago by
Ram
37k • written 7.7 years ago by
bioinfo
▴ 60
0
votes
5
replies
558
views
Create phylogenetic tree of 144 species
phylogenetic-tree
updated 14 hours ago by
Ram
37k • written 5 weeks ago by
anasjamshed1994
▴ 120
0
votes
3
replies
465
views
Merging compressed fastq files based on a conditions defined in a csv file
bash
linux
updated 13 hours ago by
Ram
37k • written 12 months ago by
D
• 0
2
votes
3
replies
457
views
samtools mpileup error - 1 samples in 1 input files
samtools
bioinformatics
SAM
BAM
mpileup
updated 17 hours ago by
Pierre Lindenbaum
152k • written 13 months ago by
joseph.kelly.94
▴ 10
0
votes
1
reply
390
views
sorting clusters from cd hit
cd-hit
updated 13 hours ago by
Ram
37k • written 5 weeks ago by
Nabil
• 0
0
votes
1
reply
348
views
How can I find high copy number sequence in Bacteria genome?
Bacteria
updated 13 hours ago by
Ram
37k • written 11 months ago by
amirsangi2628
• 0
1
vote
1
reply
340
views
Getting a PhD in Bioinformatics only having a BSc in Data Science
software-development
project
updated 13 hours ago by
Ram
37k • written 12 months ago by
d
• 0
0
votes
1
reply
285
views
Finding AIC using R for best DNA models and open MSA on web browser on given multisequence fasta file.
msa
R
updated 13 hours ago by
Ram
37k • written 11 months ago by
Platelet Guardian
• 0
0
votes
1
reply
277
views
How to calculate 2.5% pvalues for the 2 ends of the distribution?
numpy
t-test
python
genomics
updated 13 hours ago by
Ram
37k • written 6 weeks ago by
Virat_Baahubali
• 0
0
votes
13
replies
276
views
RNAseq for DE purpose
RNAseq
updated 11 hours ago by
swbarnes2
13k • written 15 hours ago by
m.habib
• 0
1
vote
1
reply
271
views
How do I subset a dataframe based on several other dataframes using R?
R
affymetrix
updated 13 hours ago by
Ram
37k • written 12 months ago by
melissachua90
▴ 40
0
votes
4
replies
261
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
17 hours ago by
Sarah
• 0
0
votes
0
replies
240
views
How to select the best gene/transcriptomics from multiple hits?
Genome
Annotation
Plastid
OGDRAW
updated 14 hours ago by
Ram
37k • written 6 weeks ago by
a.bibek52
• 0
0
votes
3
replies
234
views
Change accession number to chromosome number in reference genome
fasta
chromosome
updated 15 hours ago by
Ram
37k • written 1 day ago by
Tsigabu
• 0
0
votes
3
replies
206
views
bwa-meth unrecognized reference name during sam_parse
EM-seq
Methyl-seq
alignment
bwa-meth
updated 18 hours ago by
GenoMax
125k • written 6 days ago by
bp22
▴ 20
0
votes
0
replies
198
views
Comparing mapped reads between long-read bulk RNA-seq samples
transcriptomics
RNA-seq
TPM
long-read
updated 13 hours ago by
Ram
37k • written 6 weeks ago by
ghs101
• 0
2
votes
0
replies
195
views
Should one concatenate two haplotype genome assemblies into one assembly?
PacBio
genome-assembly
whole-genome-sequence
Hi-C
updated 13 hours ago by
Ram
37k • written 11 months ago by
anikcropscience
▴ 150
0
votes
0
replies
190
views
Comparative genomic analysis for domestication related traits
genomics
updated 14 hours ago by
Ram
37k • written 4 weeks ago by
shwetamgr1
▴ 10
0
votes
1
reply
162
views
Identifying whether a sequence is Novel or not
Novel-sequence
WGS
updated 14 hours ago by
Ram
37k • written 11 days ago by
Mustafa
• 0
0
votes
3
replies
160
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
updated 6 hours ago by
seidel
10k • written 16 hours ago by
bioinformatics.girl
• 0
3
votes
2
replies
154
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 18 hours ago by
rpolicastro
11k • written 1 day ago by
janinubinu
• 0
0
votes
1
reply
153
views
How to analysis genomes with orthologs?
ortholog
genome
annotation
updated 22 hours ago by
GenoMax
125k • written 1 day ago by
沛煒
• 0
0
votes
0
replies
140
views
Scanpy - highest expressed genes
normalization
Scanpy
scRNA
updated 14 hours ago by
Ram
37k • written 4 days ago by
mt_pereira
• 0
2
votes
2
replies
137
views
Analyzing bulk RNA-seq
RNAseq
updated 12 hours ago by
swbarnes2
13k • written 14 hours ago by
Zaid
• 0
0
votes
0
replies
129
views
Normalizing expression values
normalization
Scanpy
logCPM
scRNA
updated 14 hours ago by
Ram
37k • written 4 days ago by
mt_pereira
• 0
0
votes
0
replies
113
views
Bootstrap in PhyML
phyml
bootstrap
23 hours ago by
Jimpix
▴ 10
1
vote
1
reply
94
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 15 hours ago by
Ram
37k • written 18 hours ago by
Aidand
• 0
0
votes
0
replies
75
views
Remove duplicates in multifasta, where entries are paired
bash
python
17 hours ago by
SaltedPork
▴ 170
0
votes
0
replies
75
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
10 hours ago by
bioinfo
▴ 20
0
votes
1
reply
70
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
updated 2 hours ago by
barslmn
★ 1.2k • written 3 hours ago by
ibq.enriquepola
• 0
0
votes
0
replies
69
views
VNTR genotyping
NGS
VNTR
genotyping
11 hours ago by
Genotepes
▴ 950
0
votes
0
replies
66
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
12 hours ago by
CH1374
▴ 10
0
votes
0
replies
65
views
Trimmomatic
RNA
check
quality
fastaq
Trimmomatic
10 hours ago by
Monia
• 0
0
votes
0
replies
63
views
Combining mRNA and total RNA studies
RNA-Seq
bulk
updated 15 hours ago by
Ram
37k • written 19 hours ago by
aksh
• 0
0
votes
0
replies
62
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
12 hours ago by
a.bibek52
• 0
0
votes
0
replies
62
views
High downstream gene expression
downstream
High
Gene
expression
3 hours ago by
yoser4
▴ 10
0
votes
0
replies
61
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase
off-target
SNPS
WGS
dCas9
15 hours ago by
pd378
• 0
0
votes
0
replies
61
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
12 hours ago by
a.bibek52
• 0
0
votes
0
replies
59
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq
deseq2
ampliseq
ion-torrent
R
19 hours ago by
Fernando
• 0
0
votes
0
replies
58
views
Twist Exome Sequencing Data: Palindromic Tandem Insertion-Deletion
NGS
Artefact
Twist
Sequencing
Exome
20 hours ago by
TraPS-VarI
• 0
55 results • Page
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Recent Votes
Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: IGV coverage bar has color, but no mutation?
Answer: What is the difference between a Read and a Fragment in RNA-seq?
lncRNA analysis tutorial
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
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Comment: How to extract the list of genes from TCGA CNV data
by
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84k
Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
Comment: RNASeq differential expression masked by pathways disregulation
by
ATpoint
68k
If this is the case then you cannot correct for anything as this effect is nested with center.
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
That error message is very descriptive. Could you also add the line 997531?
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴ 110
Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
Comment: Is the heterozygosity flag (--het) in vcftools calculate observed and expected h
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dr.fakharunnisa
• 0
Hello #gubrins Have you found the answer
Comment: CoveragePlot in Signac from MACS2 Object
by
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10k
The `object` will the the Seurat object you're working with, because that contains the data that will be plotted (Tn5 insertion events per …
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date
by
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125k
Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong. $ esearch -db nu…
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Mensur Dlakic
★ 22k
Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
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Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
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Hi jv, Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
by
Jiyao Wang
▴ 290
You can also try out [iCn3D](https://structure.ncbi.nlm.nih.gov/icn3d). After you load your custom PDB via the menu "File > Open File > PDB…
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
• 0
What is 'peaks' entered as?... The input is: CoveragePlot( object = pbmc, region = "CD8A", ranges = peaks, …
Comment: Faking hh-suite workflow / alignment output
by
Nick
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I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
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10k
Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
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swbarnes2
13k
Honestly, I think most RNASeq aligners are fairly robust to adapters. You could probably get away with not trimming at all
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