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458 results • Page
1 of 10
Sort: Rank
Rank
Views
Votes
Replies
0
votes
6
replies
202
views
How to find promoter sequence of a gene?
promoter
updated 21 minutes ago by
Trivas
▴ 690 • written 15 hours ago by
sunyeping
▴ 40
0
votes
0
replies
16
views
ImportError: Bio.Alphabet has been removed from Biopython
Biopython
updated 1 hour ago by
GenoMax
127k • written 1 hour ago by
Neel
▴ 10
0
votes
0
replies
11
views
ExomeDepth installation error
ExomeDepth
Exome
CNV
1 hour ago by
Medha
• 0
0
votes
0
replies
55
views
PCA in gene expression
TCGA-
PCA
3 hours ago by
ali
• 0
0
votes
0
replies
47
views
Can't initialise orthomcl schema at orthomclInstallschema step.
mysql
perl
orthomcl
4 hours ago by
shivankparashar
• 0
1
vote
2
replies
148
views
Informations for gene summary are missing in eutils api of NCBI?
NCBI
esummary
eutils
Gene
6 hours ago by
dare_devil
★ 1.7k
2
votes
2
replies
126
views
correlations in R
cor
R
6 hours ago by
rene.j.erhardt
▴ 10
1
vote
2
replies
138
views
Weird looking dispersion & MA plot?
MA
dispersion
plot
deseq2
seq
rna
updated 4 hours ago by
ATpoint
70k • written 13 hours ago by
Neha
• 0
0
votes
0
replies
76
views
BCFtools for somatic vs. germline variant calling
RNA-seq
germline
calling
bcftools
variant
13 hours ago by
rebeliscu
▴ 50
0
votes
0
replies
83
views
Error with a function in ATAC-seq analysis
ATAC-seq
14 hours ago by
Chris
▴ 70
0
votes
0
replies
67
views
how to get genomic range for hi-c datasets in hdf5 file
hi-c
genomic
map
contact
ranges
R
15 hours ago by
rheab1230
▴ 140
0
votes
0
replies
71
views
Samtools: remove unmapped reads as well as reads that are mapped incorrectly
samtools
updated 15 hours ago by
Ram
38k • written 15 hours ago by
npavliukovec
• 0
0
votes
0
replies
59
views
how to interpret hi-c heatmap hdf5 file
heatmap
maps
hdf5
hi-c
16 hours ago by
rheab1230
▴ 140
0
votes
6
replies
224
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 2 hours ago by
GenoMax
127k • written 18 hours ago by
Human
• 0
0
votes
0
replies
70
views
Gain of function amplifications - CCLE/cBioPortal
copy
gains
amplification
number
cBioPortal
CCLE
18 hours ago by
Lakshmi
▴ 10
0
votes
0
replies
68
views
Biomark Fluidigm delta delta CT method calculation
Fluidigm
Biomark
qPCR
18 hours ago by
jms2520
▴ 20
0
votes
0
replies
71
views
pyscenic cannot mapped to the feather file
pyscenic
19 hours ago by
Andy
▴ 30
0
votes
0
replies
68
views
How to calculate Summary.csv statistics after re-running STARSolo cell filtering?
scRNA-seq
STARSolo
STAR
19 hours ago by
ayeTown
• 0
0
votes
0
replies
81
views
Solving set of equations possibly with Matlab for affinity measurement with ELISA
set
ELISA
affinity
Matlab
equation
20 hours ago by
field654
▴ 30
0
votes
0
replies
81
views
how to get the nucleotide squence behind a symbolic ALT in VCF
SV
vcf
sniffles
20 hours ago by
Maxine
• 0
0
votes
0
replies
131
views
How can I retrive the actual amino acid and the alternative amino acid (if any cordon changes happened due to editing)?
RNA
editing
21 hours ago by
Genetics
▴ 20
0
votes
0
replies
76
views
pyscenic feather file
pyscenic
21 hours ago by
Andy
▴ 30
1
vote
1
reply
132
views
Is there a site that takes a list of uniprot IDs/gene IDs as input and create radial phylogenetic tree?
phylogenetictree
18 hours ago by
Diwan
▴ 650
0
votes
0
replies
77
views
Something wrong with my code concerning bsseq visualization
bsseq
plotRegion
R
22 hours ago by
diqixiaoyaoer
▴ 10
0
votes
0
replies
81
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
22 hours ago by
Manav
• 0
0
votes
3
replies
172
views
TSV with multi-allelic sites to VCF
bcftools
updated 8 hours ago by
barslmn
★ 1.3k • written 1 day ago by
Christian
▴ 20
0
votes
0
replies
85
views
Spearman correlation rna-seq gene to blood values
spearman
rna-seq
updated 1 day ago by
Hemal
• 0 • written 1 day ago by
bas2020
▴ 20
0
votes
0
replies
68
views
Outgroup for plastome NJ-tree (from pseudoalignment based on SNPs)
bwa-mem2
samtools
freebayes
mega
vcf2phylip
1 day ago by
poecile.pal
▴ 50
4
votes
3
replies
157
views
Geom bar postive and negative values in a flipped plot
flip_coord
ggplot
geom_bar
4 hours ago by
luzglongoria
▴ 40
3
votes
8
replies
261
views
getting coding exon information from Ensembl API
Ensembl
API
updated 20 hours ago by
Ram
38k • written 1 day ago by
Nobody
▴ 30
0
votes
0
replies
95
views
displaying results of different RNA-seq projects in R shiny
RNA-seq
shiny
R
1 day ago by
rls_08
▴ 40
2
votes
2
replies
134
views
RNAseq: same reads + more complete scaffold = fewer DEGs?
RNAseq
2 hours ago by
phillip.brassington
▴ 10
0
votes
0
replies
78
views
calc IBS with vcf files with different snfs
IBS
PLINK
2 hours ago by
Mali
• 0
0
votes
0
replies
79
views
Hi-C aggregation plot | ARA | PE-Scan
Hi-C
1 day ago by
Argonaut
• 0
1
vote
3
replies
151
views
Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
QC
cutadapt
Illumina
trimming
3.4
updated 1 day ago by
GenoMax
127k • written 1 day ago by
Bengisu
• 0
1
vote
3
replies
165
views
What is exactly meant by "GENCODE TSS"?
GENCODE
transcription
annotation
TSS
gene
20 hours ago by
ConvolutedGenome
▴ 10
0
votes
3
replies
171
views
SRA Taxonomy Analysis - difference between tables and web
athena
taxonomy
sra
cloud
updated 2 hours ago by
GenoMax
127k • written 1 day ago by
Art_SG
• 0
0
votes
0
replies
90
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
1 day ago by
rheab1230
▴ 140
0
votes
2
replies
149
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
22 hours ago by
Sian
• 0
3
votes
4
replies
245
views
Creating sample groups from a combination of genes for survival analysis
Survival
1 day ago by
krushnach80
★ 1.1k
3
votes
2
replies
148
views
Power analysis for patient samples
RNA-seq
1 day ago by
aropri
▴ 130
0
votes
2
replies
144
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
1 day ago by
HERMAN
▴ 10
0
votes
1
reply
127
views
Error when using compareCluster from enichment
compareCluster
updated 1 day ago by
Basti
★ 1.4k • written 1 day ago by
jacob
• 0
0
votes
0
replies
93
views
Need Help Scraping MeSH terms from Pubmed
Python
Entrez
Scraping
updated 1 day ago by
Ram
38k • written 1 day ago by
Arnau
• 0
1
vote
1
reply
117
views
NA14622 data for benchmarking
benchmarking
vcf
bed
GiAB
updated 1 day ago by
GenoMax
127k • written 1 day ago by
emmanouil.a
▴ 110
0
votes
2
replies
161
views
How to add gene information below the BSmooth result ?
BSmooth
methylation
DNA
1 day ago by
diqixiaoyaoer
▴ 10
1
vote
1
reply
138
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot
phyloseq
plot
abundance
ggplot2
R
updated 1 day ago by
Basti
★ 1.4k • written 1 day ago by
flourde
• 0
1
vote
5
replies
297
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 1 day ago by
Trivas
▴ 690 • written 2 days ago by
TJay
• 0
1
vote
1
reply
130
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 2 days ago by
Pierre Lindenbaum
153k • written 2 days ago by
rj.rezwan
• 0
0
votes
0
replies
99
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
2 days ago by
zhangfish
▴ 40
458 results • Page
1 of 10
Recent Votes
Comment: Run nextflow sections sequentially
Answer: Differences between BioMart and Ensembl site
Answer: Differences between BioMart and Ensembl site
Comment: Run nextflow sections sequentially
Comment: Differences between BioMart and Ensembl site
Comment: Run nextflow sections sequentially
Comment: correlations in R
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Recent Replies
Comment: How to find promoter sequence of a gene?
by
Trivas
▴ 690
You can use the UCSC genome browser to get the the sequence of X bases upstream of a gene, then use tools in MEME-suite/JASPAR to look for …
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
Hello Jeo, We found that Jun/fos are highly expressed in RNAseq. But to map reads mapping to regions upstream of genes, do you mean ATAC…
Comment: significant sequence identity?
by
xuechun
• 0
Is there have any papers to support these? Will you share some reporters?
Comment: Does it possible to know what are the adjacent genes up to 1000bp upstream and
by
Neel
▴ 10
Thank You Sir for your reply.
Comment: Does it possible to know what are the adjacent genes up to 1000bp upstream and
by
Neel
▴ 10
Thank you for your reply...
Comment: Differences between BioMart and Ensembl site
by
jpuntomarcos
▴ 40
Thanks! I would suggest adding a small explanation/note, probably in the RefSeq column tooltip.
Comment: How to find promoter sequence of a gene?
by
Matthias Zepper
3.4k
Please describe in more detail what kind of input you have and which organism you are working with. As a rule of thumb, everything betwee…
Comment: Differences between BioMart and Ensembl site
by
jpuntomarcos
▴ 40
Yes, both are GRCh37.p13. [This is the link to the Biomart query][1] (you have to click Results), but I don't know how long the link will w…
Answer: Differences between BioMart and Ensembl site
by
Ben_Ensembl
★ 2.2k
Hi jpuntomarcos, The transcript table you have observed will only show you a single RefSeq transcript that is mapped per Ensembl transcr…
Comment: SRA Taxonomy Analysis - difference between tables and web
by
GenoMax
127k
There have always been differences in web based results from NCBI and what you may get from command line tools. In this case if the data co…
Comment: how to get to a VCF from bam files
by
GenoMax
127k
You are using an ancient version of bcftools (from 2016). Current version is 1.17. Please ask your system admins to upgrade, if that is the…
Comment: Differences between BioMart and Ensembl site
by
GenoMax
127k
Looks like you linked GRCh37 site for Ensembl. Are you using the same genome build in BioMart?
Comment: Alignment REST API
by
Shred
★ 1.0k
Just check what they'd implemented so far in their script (for example, in the `clientPool` function).
Comment: Run nextflow sections sequentially
by
colindaven
4.6k
@Raygozak Please be nice to the people who have provided you with answers and have some humility. I understand exactly what they mean, and …
Comment: How to include spatial coordinate data into anndata within scanpy
by
Omics data mining
▴ 210
I tried to separately include the "spatial" cooridnates and images into adata. 1) Adding tissue coodinates : c = scanpy.read_h5ad("…
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