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675 results • Page
2 of 14
Sort: Views
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Views
Votes
Replies
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R
software error
sequencing
genome
updated 10 days ago by
GenoMax
142k • written 3.2 years ago by
gs000095
▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 23 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 29 days ago by
ATpoint
82k • written 4 weeks ago by
BioinfGuru
★ 1.7k
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 4 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 14 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 16 days ago by
e.r.zakiev
▴ 210 • written 3.9 years ago by
n.anuragsharma
▴ 40
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
4 days ago by
Arton
▴ 10
1
vote
2
replies
1.7k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 10 days ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 15 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 11 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 20 hours ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 21 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
3
votes
8
replies
1.4k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 29 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 6 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient
molecule
at
bam
DNA
RG
ends
clipping
damage
updated 11 days ago by
chenl
▴ 10 • written 2.5 years ago by
Martyna
• 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 23 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
14 days ago by
Zhenyu Zhang
★ 1.2k
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
17 days ago by
eebloom
▴ 80
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
14 days ago by
Ibrahim Tanyalcin
★ 1.2k
2
votes
9
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
11 hours ago by
LauferVA
4.2k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
25 days ago by
DKA
▴ 40
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 20 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 0
2
votes
3
replies
1.0k
views
Method to detect genome doubling
CNV
genome doubling
updated 27 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
13
votes
14
replies
987
views
High Malat-1 expression in single cell data
single-cell
updated 11 days ago by
t.montserrat.ayuso
▴ 40 • written 20 days ago by
carolofharvest
▴ 40
7
votes
16
replies
971
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
20 days ago by
Ruqaiya
• 0
1
vote
8
replies
961
views
Adding CB tag to bam file
samtools
bam
updated 24 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
Maria
• 0
2
votes
5
replies
958
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 20 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
2
votes
9
replies
946
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 26 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
1
vote
10
replies
901
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 13 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
4
votes
11
replies
901
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 26 days ago by
LauferVA
4.2k • written 27 days ago by
dominickd
• 0
0
votes
2
replies
868
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 25 days ago by
barslmn
★ 2.2k • written 2.8 years ago by
jhy
▴ 10
2
votes
3
replies
854
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 15 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
10
votes
14
replies
820
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 12 days ago by
GenoMax
142k • written 18 days ago by
nicole.kavanagh
• 0
4
votes
6
replies
813
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 22 days ago by
dsull
★ 6.0k • written 26 days ago by
qudrat.nii
▴ 10
0
votes
1
reply
806
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 17 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
1
vote
5
replies
803
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
3
replies
803
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 3 days ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
2
votes
5
replies
798
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 29 days ago by
Jesse
▴ 770 • written 4 weeks ago by
Ann
★ 2.4k
0
votes
1
reply
787
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 21 days ago by
Francesco
▴ 10 • written 3.4 years ago by
gt
▴ 30
4
votes
8
replies
775
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 22 days ago by
Alex Reynolds
35k • written 23 days ago by
J
▴ 10
0
votes
3
replies
775
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 20 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
8
votes
8
replies
770
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 24 days ago by
swbarnes2
14k • written 25 days ago by
Aaliya
▴ 10
3
votes
6
replies
766
views
Ciriquant not configuring hisat2 indexed files
ciriquant
27 days ago by
Atul K.
• 0
3
votes
4
replies
762
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
27 days ago by
rahu
• 0
3
votes
3
replies
758
views
KissDE and batch effect
kissDE
kissplice
27 days ago by
david.b.rombaut
▴ 10
0
votes
2
replies
756
views
homer not configured properly
Homer
makeTagDirectory
updated 16 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
1
vote
6
replies
756
views
anRichment is missing
WGCNA
anRichment
updated 13 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
1
vote
16
replies
749
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 day ago by
GenoMax
142k • written 4 days ago by
hophuquy0944
• 0
2
votes
9
replies
738
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 12 days ago by
schmince
• 0
5
votes
4
replies
732
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
25 days ago by
kirillkirilenko
▴ 40
675 results • Page
2 of 14
Recent Votes
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
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Recent Awards •
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Scholar
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Pierre Lindenbaum
161k
Voter
to
Sara
▴ 30
Popular Question
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carlopecoraro2
★ 2.5k
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scideas
▴ 30
Popular Question
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Muhammad
• 0
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synat.keam
▴ 100
Scholar
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jv
★ 1.8k
Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
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