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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
205
views
Identify genes for mapped reads with combined human-7HPV genome index
star
samtools
updated 12 days ago by
Ram
40k • written 12 days ago by
r.j.lock
• 0
0
votes
0
replies
130
views
Data for pathview() (KEGG Pathway Map) after EdgeR
EdgeR
LogFC
pathview
KEGG
12 days ago by
Ann
▴ 10
0
votes
0
replies
279
views
GTF/Reference genome adjustments? Gene-based differential expression analysis of genetically modified mouse line
RNA-seq
DGE
updated 12 days ago by
Ram
40k • written 12 days ago by
alex
• 0
0
votes
0
replies
153
views
Selecting SNPs for two-sample Mendelian randomization study/analysis
Two-sample
SNPs
Mendelian
randomization
12 days ago by
huynguyenacademia
• 0
0
votes
0
replies
145
views
cosine simialrity of mutation signature analysis
similarity
Mutational
analysis
signature
cosine
12 days ago by
probioquestioner
• 0
1
vote
1
reply
230
views
Significance testing of top vs. random SNPs
SNPs
significance
variance
statistical
updated 9 days ago by
dthorbur
▴ 560 • written 13 days ago by
am29
▴ 30
4
votes
2
replies
442
views
Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data
rna-seq
smartseq2
r
updated 10 days ago by
yhdist
▴ 70 • written 13 days ago by
Cookin
▴ 10
0
votes
0
replies
153
views
Why we are using filtering >0 for up and <0 for down after TopTags() to extract de genes ids?
EdgeR
logfc
DEG
13 days ago by
Ann
▴ 10
0
votes
1
reply
182
views
PyMOL: how to list all selection names?
pymol
updated 12 days ago by
Wayne
★ 1.8k • written 13 days ago by
Ondina
▴ 90
2
votes
2
replies
225
views
Clustering algorithm based on grouping sequences into gene families
gene-families
clustering
updated 12 days ago by
Ram
40k • written 13 days ago by
francesco
• 0
0
votes
0
replies
148
views
Homozygous reference genotype for a GIAB genome
GIAB
IDs
reference
rs
Homozygous
13 days ago by
New2R
▴ 60
0
votes
0
replies
150
views
PRSice - Phenotype File Not Read Correctly
PRSice2
13 days ago by
V
• 0
0
votes
2
replies
1.6k
views
Question about REDItools
REDItools
updated 14 days ago by
Ethan Lee
• 0 • written 4.1 years ago by
tujuchuanli
▴ 100
1
vote
5
replies
521
views
Idat raw data conversion
idat
updated 13 days ago by
Giulio Genovese
▴ 330 • written 14 days ago by
Zi
• 0
1
vote
3
replies
363
views
What is "intersectional genetic strategy"? How does it work? What can it do?
cell-subtypes
13 days ago by
Ethan Lee
• 0
0
votes
0
replies
184
views
What metrics to use to calculate variant library evenness or uniformity or bias
library-bias
variant
updated 14 days ago by
Ram
40k • written 15 days ago by
eli_bayat
▴ 90
0
votes
0
replies
211
views
Tools to turn perfect phylogenetic matrix into a tree
parsimony
Phylogeny
tree
15 days ago by
Ritu_K
▴ 10
2
votes
4
replies
450
views
Help with celltype annotation
seurat
single-cell
14 days ago by
Chris
▴ 200
0
votes
1
reply
1.0k
views
Downstream analysis on multi-sample or single-sample VCF files?
next-gen
VCF
updated 15 days ago by
Ram
40k • written 2.8 years ago by
NGSCanBioinf
▴ 10
0
votes
1
reply
660
views
How to get enrichment of ERVs in differentially expressed peaks from ATAC-seq data?
ChIP-Seq
ERVs
ATAC-seq
updated 15 days ago by
pb11
▴ 10 • written 2.8 years ago by
fdemiguelsdp
• 0
3
votes
4
replies
374
views
Weighted analysis
RNA-seq
12 days ago by
Peter
• 0
1
vote
2
replies
279
views
Multiple testing adjustment for stepwise model selection
statistics
12 days ago by
mel22
▴ 100
0
votes
2
replies
299
views
Deseq2 colData for single condition
RNA-seq
14 days ago by
Petesview
• 0
0
votes
0
replies
177
views
PopGenome: there are missing regions when calculating Tajima's D per gene
PopGenome
13 days ago by
Bing
• 0
1
vote
2
replies
292
views
functional analysis prediction
functionalanalysis
metabarcoding
16S
12 days ago by
safeassli
• 0
0
votes
1
reply
234
views
Asymmetric/biased log2FC values for low-expressed genes in DESeq2
DESeq2
DEG
fold-change
updated 15 days ago by
Ram
40k • written 15 days ago by
chenzy
• 0
0
votes
9
replies
1.0k
views
Chipseq analysis on repeat genes
galaxy
repeatmasker
ChIP-seq
repeat-elements
ATAC-seq
updated 4 days ago by
rfran010
▴ 830 • written 16 days ago by
pb11
▴ 10
0
votes
5
replies
479
views
Convert gene id's to gene symbol preserving gene id's in deseq2
ensembl
r
DE
deseq2
updated 14 days ago by
Ram
40k • written 16 days ago by
dylannicoembros
• 0
1
vote
1
reply
252
views
Bioconductor Package Installation
bioconductor
updated 16 days ago by
Ram
40k • written 16 days ago by
oduduabasi.isaiah
• 0
0
votes
0
replies
206
views
External validation in bioinformatics analyses
External
validation
16 days ago by
Saeedeh Salehi
▴ 10
2
votes
4
replies
386
views
join the control replicates
RNA-seq
updated 15 days ago by
seidel
11k • written 16 days ago by
Jean Pierre
• 0
4
votes
5
replies
508
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
13 days ago by
psm
▴ 100
0
votes
3
replies
325
views
RdRp scan - identifying/detecting viruses- metagenomic workflow- need help
RdRp
virus-detection
metagenomic
updated 12 days ago by
Ram
40k • written 16 days ago by
eric--carron
• 0
1
vote
1
reply
232
views
Is it possible to find the target bed file for TSO500 panel?
bed
illumina
target
updated 16 days ago by
GenoMax
134k • written 16 days ago by
Danchurova
• 0
0
votes
2
replies
277
views
circRNA isolation
circular-RNA
circRNA
cDNA
15 days ago by
dbagmerve
• 0
2
votes
2
replies
276
views
Pangenome using Orthofinder
OrthoFinder
Pangenome
bacteria
12 days ago by
kirankumareripogu
▴ 10
5
votes
3
replies
290
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 16 days ago by
Ram
40k • written 16 days ago by
sarahmanderni
▴ 90
1
vote
2
replies
281
views
Dotplot error: subscript out of bound
R
scRNA-seq
seurat
6 days ago by
Xuhao
• 0
0
votes
0
replies
126
views
assembly: purge_dups removes too much sequence
purge_dups
assembly
nanopore
repeats
plants
16 days ago by
colindaven
5.5k
0
votes
7
replies
942
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 4 days ago by
rfran010
▴ 830 • written 17 days ago by
ccbb7aab4
▴ 20
0
votes
0
replies
122
views
Paired vs Unpaired t-test: Compositional analysis in the Human snRNA-seq data
snRNA-seq
scRNA-seq
analysis
statistic
compositional
16 days ago by
joonhong kwon
▴ 50
0
votes
0
replies
125
views
how simply mutation annotation in R?
annotation
RNA-seq
Bioconductor
16 days ago by
octpus616
▴ 90
0
votes
2
replies
236
views
NCBI nt seqid2taxid.map
ncbi
kraken2
kraken
database
17 days ago by
Gio
• 0
0
votes
3
replies
263
views
CNV using GISTIC
CNV
GISTIC
updated 17 days ago by
Ram
40k • written 17 days ago by
ananta.kapoor
• 0
0
votes
0
replies
138
views
rDNA copy number variation (CNV) based on hg38
hg38
CNVkit
rDNA
CNV
genomics
17 days ago by
rbioinfo
▴ 10
0
votes
4
replies
310
views
Split reads along the genome in my samples
DNA
sequencing
17 days ago by
paulaotero.sanchez
• 0
0
votes
0
replies
135
views
Issue in creating Gene Regulatory Network links using CellOracle
Python
CellOracle
GRN
15 days ago by
Debashish
• 0
0
votes
0
replies
135
views
Cluster files from 2018-2020 archive of PDB
database
PDB
archive
Structural
17 days ago by
yhdist
▴ 70
0
votes
4
replies
288
views
Analyzing time-patterns in RNA Seq data only having results_apeglm
R
sequencing
17 days ago by
Paul
• 0
0
votes
0
replies
133
views
qtlseq oserror 38
qtlseq
15 days ago by
지헌
• 0
1,000 results • Page
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Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
GenoMax
134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
Alex Reynolds
35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
• 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
• 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File
by
Reem
• 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR
by
Trivas
★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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