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503 results • Page
3 of 11
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Votes
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0
votes
0
replies
113
views
pathwaycommons SPARQL endpoint down?
pathwaycommons
6 days ago by
mk
▴ 270
0
votes
3
replies
241
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicFeatures
ORFik
GenomicRanges
updated 6 days ago by
Ram
37k • written 6 days ago by
Estefania
▴ 10
0
votes
6
replies
316
views
Getting a VCF file from plink .bed, .fam and .bim files
vcf
plink
4 days ago by
hi.there
• 0
1
vote
3
replies
284
views
Calculating PRS in a large cohort
PRS
4 days ago by
haasroni
• 0
0
votes
3
replies
197
views
Downloading 450k methylation data from GEO
minfi
450K
IDAT
Methylation
GEO
updated 6 days ago by
GenoMax
125k • written 6 days ago by
Edward E-B
• 0
0
votes
0
replies
104
views
seurat: Average expression function and find markers DE fold changes do not add up
Seurat
Single-Cell
updated 6 days ago by
Ram
37k • written 6 days ago by
rasing02
• 0
0
votes
3
replies
192
views
Help interpreting FastQC report
fastQC
trimming
quality-control
updated 6 days ago by
GenoMax
125k • written 7 days ago by
sithlordashley
• 0
0
votes
0
replies
105
views
DepthOfCoverage badly formed genome location error
coverage
7 days ago by
User000
▴ 620
0
votes
0
replies
72
views
Combination of genomic datasets genotyped using different arrays
genotyping
GWAS
imputation
inflation
7 days ago by
desicasares
▴ 10
0
votes
3
replies
197
views
Error while using rpy2
R
rpy2
Python
updated 4 days ago by
Wayne
★ 1.6k • written 7 days ago by
sidrah.maryam
▴ 40
0
votes
0
replies
80
views
Getting additional positive regulons on enabling --all_modules option in pySCENIC
BioinformaticsTool
Regulon
scRNA-Seq
SCENIC
GRN
pySCENIC
7 days ago by
Nitin Narwade
★ 1.3k
0
votes
0
replies
81
views
SNP data - significance heterozygosity test?
significance
test
SNP
7 days ago by
Roland
▴ 10
0
votes
1
reply
159
views
Compare population structure results
plots
circlize
dendextend
R
updated 6 days ago by
size_t
▴ 40 • written 7 days ago by
waqaskhokhar999
▴ 150
0
votes
0
replies
136
views
Prediction of SSU, LSU, and ITS regions from genome assembly that related together
ITS
LSU
SSU
7 days ago by
ALI Hkz
• 0
0
votes
0
replies
127
views
Gene signature with Machine Learning and Single Cell RNA-seq ?
Cancer
RNA-seq
signature
Cell
Gene
Machine
Learning
Single
7 days ago by
AKypR
• 0
0
votes
1
reply
235
views
Plink duplicate ID
Plink
updated 7 days ago by
Viktor Messi
• 0 • written 21 days ago by
Aswr
• 0
1
vote
3
replies
228
views
Variant effect predictor in ictalurus punctatus
VariantEffectPredictor
VEP
updated 7 days ago by
barslmn
★ 1.2k • written 7 days ago by
Hayler Edu
▴ 30
0
votes
2
replies
203
views
merging and annotating bcf files for variant calling
vcf
bcf
calling
bcftools
variant
6 days ago by
pr.khavari
• 0
1
vote
3
replies
309
views
MesKit error message - Join columns must be present in data.
MesKit
R
updated 5 days ago by
Ram
37k • written 7 days ago by
CH1374
▴ 10
1
vote
2
replies
197
views
How to install pandas
ml
python
offtopic
updated 6 days ago by
Ram
37k • written 7 days ago by
Sargun
• 0
0
votes
0
replies
145
views
Scanpy - highest expressed genes
normalization
Scanpy
scRNA
updated 3 days ago by
Ram
37k • written 8 days ago by
mt_pereira
• 0
0
votes
0
replies
135
views
Normalizing expression values
normalization
Scanpy
logCPM
scRNA
updated 3 days ago by
Ram
37k • written 8 days ago by
mt_pereira
• 0
0
votes
0
replies
144
views
Machine Learning Classifiers on TCGA dataset(tpm_unstrand) gene expression data set
machine
RNASeq
python
learning
8 days ago by
Jakpa
▴ 50
0
votes
0
replies
142
views
getTable ignores query ranges
rtracklayer
8 days ago by
Kyle
• 0
0
votes
0
replies
156
views
maximum fastq file size in galaxy?
fastq
rna-seq
usegalaxy
8 days ago by
demoraesdiogo2017
▴ 80
0
votes
0
replies
199
views
Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:....
COGs
GOs
results
Eggnog
9 days ago by
F.Bedjou
• 0
0
votes
2
replies
288
views
How possible deadlocks are there while migrating from MYISAM to InnoDb?
dbms
updated 8 days ago by
Pierre Lindenbaum
152k • written 9 days ago by
jessewhite8077
• 0
0
votes
0
replies
193
views
How quality score for somatic mutations in ICGC was calculated
somatic
mutations
ICGC
9 days ago by
caochch
• 0
0
votes
0
replies
181
views
vcf2maf - generate 1 maf for 2 vcf files
maf
WES
vcf2maf
updated 6 days ago by
Ram
37k • written 9 days ago by
CH1374
▴ 10
0
votes
1
reply
320
views
**Error: unable to open file or unable to determine types for file**
bedtools
updated 9 days ago by
Pierre Lindenbaum
152k • written 9 days ago by
Neel
▴ 10
0
votes
0
replies
196
views
Critical criteria for filtering variants by VariantFiltration
WGS
Filtration
gatk
WES
9 days ago by
Alireza
▴ 20
0
votes
0
replies
195
views
Sc-RNA seq 5’ V2 PE auto detected by CellRanger as R2 only chemistry
cellranger
5prime
PE
R2
V2
9 days ago by
ashley.fletcher2
• 0
0
votes
0
replies
147
views
transcriptome assembly, GWA, BGC
GWA
assembly
BGC
transcriptome
9 days ago by
Kiran
• 0
0
votes
0
replies
233
views
Recommended tools/packages for power and sample size estimation for microRNA gene expression and/or protein expression study?
Power
protein
miRNA
sample
analysis
size
9 days ago by
Lalaland
▴ 30
2
votes
1
reply
255
views
bgzip error 4
bgzip
error4
vcf
updated 9 days ago by
Pierre Lindenbaum
152k • written 9 days ago by
yb
▴ 10
0
votes
1
reply
613
views
pooled-heterozygosity calculation
VCF
Population-Genetics
WGS
Selective-sweep
updated 9 days ago by
mmcui0018
• 0 • written 15 months ago by
reza
▴ 300
0
votes
4
replies
283
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
3 days ago by
Sarah
• 0
5
votes
14
replies
690
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
updated 5 days ago by
Jeremy Leipzig
21k • written 9 days ago by
Emoji
• 0
0
votes
0
replies
144
views
tximeta accessing gene symbols after addIds()
deseq2
symbols
tximeta
gene
9 days ago by
iddryg
• 0
1
vote
1
reply
171
views
How to set NCBI entrez to pipe or ignore errors?
NCBI
Entrez
updated 9 days ago by
GenoMax
125k • written 9 days ago by
rijan_dhakal
• 0
1
vote
1
reply
194
views
Aggregate gene expression
AggregateExpression
RNASeq
Seurat
expression
gene
updated 9 days ago by
jv
▴ 780 • written 9 days ago by
Anst
▴ 30
0
votes
3
replies
228
views
bwa-meth unrecognized reference name during sam_parse
EM-seq
Methyl-seq
alignment
bwa-meth
updated 4 days ago by
GenoMax
125k • written 9 days ago by
bp22
▴ 20
0
votes
0
replies
138
views
Proloc and readMSnSet
readMSnSet
proloc
9 days ago by
ciaki
• 0
0
votes
0
replies
115
views
Move Cytoscape "CytoscapeConfiguration" directory
cytoscape
9 days ago by
Lucy
▴ 110
0
votes
3
replies
263
views
best way to learn bash scripting
bash
coding
sequncing
updated 9 days ago by
Jeremy
▴ 740 • written 10 days ago by
rj.rezwan
• 0
0
votes
0
replies
151
views
Differential Peak Analysis for a specific gene using only bigWig + BED files?
differential
peak
bigwig
chip-seq
analysis
10 days ago by
Maycon
• 0
1
vote
0
replies
120
views
Meta-analysis of rare variant SAIGE-GENE output for WGS data
meta-analysis
rare
SAIGE
variant
10 days ago by
tacrolimus
▴ 100
2
votes
4
replies
283
views
Retrieve specific fasta sequences from a group of assemblies
CDS
gene
sequence
7 days ago by
SushiRoll
▴ 100
0
votes
0
replies
146
views
Add column in Obs. in anndata using scanpy
scanpy
9 days ago by
Nai
▴ 20
0
votes
0
replies
170
views
adding a heatmap to GOChord?
GOterms
plot
GOplot
R
Chord
10 days ago by
adrija.kalvisa
• 0
503 results • Page
3 of 11
Recent Votes
Answer: What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: How can I convert this pairwise format to fasta?
Answer: How can I convert this pairwise format to fasta?
Piping bowtie2 output directly into BAM
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
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Recent Replies
Comment: Size of two scRNA-Seq conditions
by
rpolicastro
11k
More important would be the cell QC stats (such as reads per cell and number of unique features detected per cell), the number of cells per…
Answer: What type of database does gnomAD use?
by
Jeremy Leipzig
21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
by
Basti
★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box
by
Ram
37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function
by
jv
▴ 780
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
• 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans
by
GenoMax
125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
by
jv
▴ 780
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content
by
jv
▴ 780
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq
by
Genetics
• 0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me. Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content
by
khoojj
• 0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads. I have checked that NEBN…
Comment: Novogene somatic results with GATK mutect2
by
GenoMax
125k
Did you look in the header of the provided VCF to see if any information has been encoded there (e.g. command line/options used).
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴ 110
That's exactly what I've done. However the dispersion is really high (primary samples) and the total number of samples seems really low to…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
If the library was made using tagmentation then you will see that pattern. Flag warnings on FastQC do not immediately indicate that the da…
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