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699 results • Page
1 of 14
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
3
views
Results of NOT FOUND encountered when running SCENIC
SCENIC
20 minutes ago by
smilewang997700
• 0
4
votes
12
replies
833
views
6 follow
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 51 minutes ago by
Gordon Smyth
★ 7.2k • written 13 days ago by
egascon
• 0
0
votes
0
replies
33
views
monocle3 dot plot by groups and each cell types
monocle3
R
4 hours ago by
sooni
▴ 20
3
votes
3
replies
122
views
help in changing Y scale in R
ggplot2
R
updated 4 hours ago by
LauferVA
4.2k • written 8 hours ago by
Ghada
• 0
2
votes
1
reply
75
views
Intersection of multiple vcf files
isec
vcf
bcftools
updated 6 hours ago by
Jeremy Leipzig
22k • written 7 hours ago by
avelarbio46
▴ 30
4
votes
2
replies
154
views
when I use htslib to write a bam. Error of "truncated file" shows by samtools
bam
htslib
2 hours ago by
Aaron
▴ 10
0
votes
0
replies
44
views
Using a within population reference genome - Recombination
relernn
vcf
popgen
recombination
8 hours ago by
dylan
• 0
0
votes
0
replies
65
views
NCBI vs Ensembl - Ortholog genes Information
Genomics
Orthologs
NCBI
Ensembl
updated 9 hours ago by
Pierre Lindenbaum
162k • written 9 hours ago by
José
▴ 10
1
vote
0
replies
62
views
Why does WGCNA use weighted correlation instead of Pearson correlation?
wgcna
12 hours ago by
絶望燃やし
▴ 10
3
votes
5
replies
178
views
I cannot download VG in any way
vg
vgteam
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
gforg34
▴ 10
0
votes
0
replies
51
views
reference geome gaf file obsolent GO replacement
gaf
GO
14 hours ago by
Nicolas
• 0
0
votes
1
reply
103
views
Can I count UMI-barcode combination without mapping?
HyDrop
protein
UMI
UMI-Tools
updated 3 hours ago by
GenoMax
142k • written 14 hours ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
134
views
How do I check if a DNA sequence of a gene is supported by RNAseq data?
Genetics
RNA-seq
Phase-variation
Alignment
14 hours ago by
Jack
• 0
0
votes
4
replies
704
views
Illumina EPIC v2 IlmnIDs and probe names
Illumina
EPIC
EPICv2
updated 15 hours ago by
Papyrus
★ 2.9k • written 6 months ago by
christine.a.pedersen
▴ 10
3
votes
6
replies
244
views
Best practices in Fungal Genome Assembly
illumina
assembly
nanopore
genome
8 hours ago by
Umer
▴ 50
0
votes
1
reply
170
views
Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
updated 16 hours ago by
GenoMax
142k • written 19 hours ago by
Ian
6.0k
2
votes
1
reply
142
views
Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
updated 17 hours ago by
ATpoint
82k • written 20 hours ago by
ev97
▴ 20
1
vote
9
replies
379
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 7 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
0
votes
0
replies
67
views
Regarding ENSEMBL/Gencode and UCSC differences (ATAC-seq, ChiPseeker peaks annotation)
ATAC-seq
CHiPseeker
Annotation
20 hours ago by
Manko47
• 0
3
votes
7
replies
453
views
Z score
Z-score
updated 20 hours ago by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
1
vote
2
replies
166
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
17 hours ago by
ashaneev07
▴ 20
2
votes
2
replies
350
views
Annotating single cell data automatically
single-cell
updated 22 hours ago by
Nat.Nataren
▴ 20 • written 5 weeks ago by
Gerard
• 0
0
votes
0
replies
70
views
EXOME DEPTH - CNV
CNV
23 hours ago by
Neha
• 0
0
votes
2
replies
145
views
coding and non-coding region of the viral genome
viral-genome
10 hours ago by
Ghada
• 0
2
votes
2
replies
126
views
dbNSFP4.7a database format to Annovar Format?
snp
annovar
NGS
dbNSFP
updated 15 hours ago by
Ram
44k • written 23 hours ago by
Clark_BioMorgan
▴ 50
0
votes
2
replies
161
views
Salmon ~ Effective Length
Salmon
updated 18 hours ago by
GenoMax
142k • written 1 day ago by
chrisk
• 0
2
votes
3
replies
239
views
Search within posts based on tags using the Biostars API
api
meta
updated 15 hours ago by
Ram
44k • written 1 day ago by
Bálint
▴ 10
0
votes
0
replies
75
views
Funcotator gnomAD incoherent number of output fields
gatk
gnomAD
Funcotator
updated 14 hours ago by
Ram
44k • written 1 day ago by
jaime alvarez
▴ 30
0
votes
1
reply
143
views
Help with proteomics downstream analysis
mass-spectrometry
proteomics
updated 1 day ago by
Ram
44k • written 1 day ago by
Álvaro
• 0
1
vote
2
replies
203
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
7 hours ago by
Ngrin
• 0
0
votes
0
replies
75
views
Calculating F_IS, F_IT on ancient DNA
adna
1 day ago by
devenvyas
▴ 740
0
votes
0
replies
76
views
The number of region with the motif sequence is different between HOMER outputs
findMotifsGenome
HOMER
annotatePeaks
1 day ago by
Aki
▴ 20
3
votes
3
replies
865
views
Cut&Run and heatmap
MACS2
bowtie2
updated 14 hours ago by
Ram
44k • written 13 months ago by
qudrat.nii
▴ 10
3
votes
12
replies
5.4k
views
7 follow
txt file to bigwig
MEME
bigwig
updated 14 hours ago by
GenoMax
142k • written 8.6 years ago by
tanni93
▴ 50
2
votes
2
replies
219
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 20 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
0
votes
2
replies
142
views
identify the coordinate for coding and non_coding region.
coding
non_coding
1 day ago by
Ghada
• 0
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 1 day ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
3
votes
2
replies
161
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 20 hours ago by
zx8754
11k • written 1 day ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
195
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
22 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
120
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
updated 11 hours ago by
Ram
44k • written 1 day ago by
Ghada
• 0
3
votes
7
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 11 hours ago by
Ram
44k • written 2.8 years ago by
Shred
★ 1.4k
0
votes
0
replies
112
views
Subset of Transcripts- How do I proceed with it?
Stringtie
updated 11 hours ago by
Ram
44k • written 1 day ago by
Varsha
• 0
1
vote
2
replies
3.8k
views
How can run cd-hit-est with a clstr threshold less than 0.8?
cd-hit
cluster
updated 1 day ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
0
votes
2
replies
262
views
Tools for chromosomal aneuploidy detection
human-genetics
aneuploidy
NGS
updated 11 hours ago by
Ram
44k • written 5 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
96
views
PyRMD
machine-learning
cheminformatics
Virtual-Screening
updated 10 hours ago by
Ram
44k • written 1 day ago by
s
• 0
3
votes
5
replies
253
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 hour ago by
MboiTui
▴ 20
0
votes
0
replies
117
views
Determining rs ids from SNP HGV base ID?
rsID
HGV
SNP
updated 1 day ago by
Ram
44k • written 2 days ago by
Katherine
• 0
0
votes
4
replies
320
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 15 hours ago by
jared.andrews07
★ 17k • written 3 days ago by
Sara
▴ 30
0
votes
1
reply
198
views
Facing problem with single cell rna seq annotation using singleR
singleR
scRNAseq
updated 10 hours ago by
Ram
44k • written 2 days ago by
sc_analysis
• 0
0
votes
0
replies
107
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
2 days ago by
kl
▴ 10
699 results • Page
1 of 14
Recent Votes
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
Answer: help in changing Y scale in R
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Comment: I cannot download VG in any way
Why does WGCNA use weighted correlation instead of Pearson correlation?
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Recent Replies
Comment: polygenic risk score
by
ashaneev07
▴ 20
Can't we calculate the prs of a single patient data with respect to GWAS data for predicting the risk for particular diseases?
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
Gordon Smyth
★ 7.2k
It is very common for studies like this to show no significant DE. Human studies like this where comparisons are made between diseases and …
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
update. The error persists. With ValidateSamFile I get no error until i use MarkDuplicates. Then for the MarkDuplicates output I get: …
Comment: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
Aaron
▴ 10
Thanks very much.
Answer: help in changing Y scale in R
by
LauferVA
4.2k
Hello @ab33b6d7 , Below is approximately the code block you provided, with a few additional lines added. Each of the new lines has > …
Comment: 2 PhD Students in single-cell bioinformatics
by
Uzma
• 0
I want to apply for this PhD position. I did MSc Zoology and MPhil biosciences.
Comment: Rseqc infer_experiment.py: 0 usable reads sampled and unknown data type
by
mazegriff
• 0
Hi pubsurfted, I ran into the same issue using a reference transcriptome with HISAT2 from the Ensembl database. For others with similar e…
Comment: Intersection of multiple vcf files
by
Jeremy Leipzig
22k
isec is pretty awful for these set operations - especially since individual samples present alleles, not lines in a VCF file. If you can co…
Comment: help in changing Y scale in R
by
Medhat
9.7k
Maybe try to calculate min and max combined_min <- min(a_filtered$value, a_filtered_tv$value, na.rm = TRUE) combined_max <- max(a_…
Answer: help in changing Y scale in R
by
ATpoint
82k
Use `+ylim(c(lower, upper))`. Either set manually, or query both `a_filtered` and `a_filtered_tv` for the minimum and maximum values that g…
Comment: Error with pheatmap - 'from' must be a finite number
by
zx8754
11k
I am not familiar with deseq data, but if it makes sense, remove rows/columns that have only NAs. #remove rows x<- mat.z[ rowSums(…
Answer: when I use htslib to write a bam. Error of "truncated file" shows by samtools
by
John Marshall
3.1k
There are several problems with this code: 1. You have not set `b->l_data`, which here should be set to the same value as `b->m_data`. T…
Comment: Best practices in Fungal Genome Assembly
by
Umer
▴ 50
Should I use both Recon and Pilon for polshing ? Recon uses Long-reads and Pilon uses short-read. if both should be used, is their any pref…
Comment: Mutation counts corrected by number of samples
by
garcesj
▴ 50
How come? If I have a pro-tumorigenic product, for example, wouldn't this comparison be valid?
Comment: How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Pac
by
Ngrin
• 0
Thanks @Zhenyu Zhang for your response. I have just looked at the files you mentioned. Do you have any recommended package or code snippet …
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