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706 results • Page
3 of 15
Sort: Rank
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Votes
Replies
0
votes
2
replies
327
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
3 days ago by
Ezequiel
• 0
2
votes
0
replies
191
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
3 days ago by
micah
▴ 30
0
votes
0
replies
120
views
problems in installing rDock
rDock
updated 2 days ago by
Ram
44k • written 4 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 4 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
731
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 4 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
385
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
142
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 4 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
Mohamed Samir
▴ 30
0
votes
0
replies
151
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
4 days ago by
Moinuddin
• 0
0
votes
1
reply
193
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Jacek
▴ 20
2
votes
1
reply
264
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 4 days ago by
Gordon Smyth
★ 7.2k • written 5 days ago by
marineandriot
• 0
0
votes
0
replies
153
views
How can i use ESM-1v ?
VEP
ESM-1v
5 days ago by
Meto
• 0
0
votes
0
replies
161
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Long
• 0
2
votes
3
replies
346
views
Trimming tool
Trimming
updated 2 days ago by
Ram
44k • written 5 days ago by
GeneC
• 0
0
votes
0
replies
152
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
5 days ago by
kilcdincer
▴ 10
0
votes
2
replies
277
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 5 days ago by
LauferVA
4.2k • written 5 days ago by
ijarne
• 0
0
votes
0
replies
169
views
genomic region of transcription factor
search
HOMER
motif
5 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
394
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 5 days ago by
dthorbur
★ 2.0k • written 6 days ago by
BATMAN
• 0
0
votes
6
replies
395
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
5 days ago by
hannes.bongartz
• 0
0
votes
0
replies
158
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 5 days ago by
GenoMax
142k • written 5 days ago by
yura.grabovska
▴ 90
4
votes
9
replies
650
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 1 day ago by
marco.barr
▴ 130 • written 7 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
214
views
constructing pangenome through psvcp
psvcp
pangenome
4 days ago by
analyst
▴ 50
1
vote
6
replies
365
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
1 day ago by
Umer
▴ 50
0
votes
4
replies
376
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 4 days ago by
txema.heredia
▴ 130 • written 6 days ago by
Ngrin
• 0
4
votes
9
replies
525
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
5 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
271
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 6 days ago by
Pierre Lindenbaum
162k • written 6 days ago by
melissachua90
▴ 70
0
votes
0
replies
140
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
6 days ago by
Varsha
• 0
0
votes
1
reply
465
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 5 days ago by
GenoMax
142k • written 6 days ago by
huxiangyulove
• 0
0
votes
0
replies
156
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
6 days ago by
O.rka
▴ 720
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 6 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
368
views
Merge clusters in Seurat UMAP
seurat
umap
6 days ago by
kilcdincer
▴ 10
0
votes
0
replies
163
views
Use of ichor CNA
Dog
CNA
genome
6 days ago by
sainavyav22
• 0
2
votes
2
replies
300
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 6 days ago by
Ram
44k • written 6 days ago by
txema.heredia
▴ 130
1
vote
0
replies
177
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 6 days ago by
Ram
44k • written 6 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
384
views
Details on salmon index
Salmon
updated 5 days ago by
Rob
6.6k • written 6 days ago by
Lorenzo
• 0
0
votes
0
replies
165
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
6 days ago by
Jsarria.EEAD
• 0
0
votes
2
replies
277
views
How can I calculate the OS of each patient?
overall-survival
2 days ago by
Pedro
• 0
1
vote
1
reply
229
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 6 days ago by
Ram
44k • written 6 days ago by
m90
▴ 30
0
votes
0
replies
158
views
cat-bgen fail
bgenix
updated 6 days ago by
Ram
44k • written 6 days ago by
lambard
• 0
3
votes
4
replies
360
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 5 days ago by
Jeremy Leipzig
22k • written 7 days ago by
Ali
• 0
3
votes
3
replies
267
views
getting exon coordinates
genomics
updated 6 days ago by
Ram
44k • written 6 days ago by
Xbox_27
• 0
0
votes
4
replies
355
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 6 days ago by
Tony
• 0 • written 7 days ago by
vk
▴ 10
1
vote
5
replies
347
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 6 days ago by
Ram
44k • written 6 days ago by
manuelmourato25
• 0
3
votes
4
replies
439
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Pierre Lindenbaum
162k
2
votes
11
replies
787
views
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
6 days ago by
egascon
• 0
1
vote
1
reply
212
views
API kegg - IndexError: list index out of range
kegg
API
updated 6 days ago by
Nyksubuz
▴ 20 • written 6 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
152
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
7 days ago by
Novogene
▴ 420
0
votes
0
replies
151
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
7 days ago by
ebertomeup
• 0
0
votes
3
replies
300
views
Sam file Header problem
Sam
Header
problem
file
updated 6 days ago by
Pierre Lindenbaum
162k • written 7 days ago by
saifulislam99121
• 0
1
vote
3
replies
310
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 6 days ago by
Ram
44k • written 7 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
602
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 7 days ago by
valdirbarth
▴ 20 • written 13 months ago by
Salomé
• 0
706 results • Page
3 of 15
Recent Votes
Comment: scRNA-seq quality control
Comment: How to get the ratio of allele counts from GATK derived VCF file?
Setting up Aspera Connect (ascp) on Linux and macOS
Setting up Aspera Connect (ascp) on Linux and macOS
Answer: Genes' fpkm values through cufflink
Answer: Genes' fpkm values through cufflink
Genes' fpkm values through cufflink
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Comment: Z score
by
Akash D
▴ 40
Ok. However, if i perform it on log2FC, there wont be any control samples visible in my heatmap. Your answer is perfect.
Comment: Z score
by
ATpoint
82k
You can apply Z-scores on whatever you want, but it must make sense and depends on what you want to do. What is the context? See for exampl…
Answer: Z score in RNAseq
by
Akash D
▴ 40
Can Z score be applied on log2FC and then visualized? Alternatively, Can log2FC be converted to Z scores and then visualized as heatmap?
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
ATpoint
82k
Just for comparison, I deal with scRNA-seq daily and my workstation is a 12700k i7 with 128GB RAM and even this is actually more than I nee…
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
by
colindaven
6.4k
- As others have said, 1-2 workstations are probably the way to go. - A Linux OS like Ubuntu is probably easiest and has best docs - RA…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
Ok, thank you for the reply. I will check out the DP field then.
Comment: Alternatives To Liftover
by
Thanujay S
• 0
Hey! Would you consider building an API for the same? Is that something you have planned?
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
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emmanouil.a
▴ 120
20k are good money for some workstations ... probably you need to run more samples at the same time ... for some 1000s you could take a wor…
Comment: samtools write-index
by
LucisTheFather
• 0
``` -o alignment.sorted.bam##idx##alignment.sorted.bam.bai ``` This portion is to get .bai index, instead of .csi indexing. Although Idk th…
Comment: samtools write-index
by
LucisTheFather
• 0
Really appreciate your help Pierre! I am a little bit confused btw. do you mean this: ``` rm -vf alignment.sorted.bam.bai minimap2 -ax map-…
Comment: samtools write-index
by
LucisTheFather
• 0
Yeah, I did multiple split tests of my pipeline (just subset 400k rows of my fastq and run through my pipeline for quick tests) and none of…
Comment: Which 1000 genomes 30x files should I use for imputation?
by
David-walson
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Hi there. Have you found any suggestions? I have alos been working on the 1KGP high coverage data, but i have no idea about how to use it p…
Comment: MAUVE: No gene annotations in Genbank file alignments
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pramach1
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The same problem persists for me too. Running progressiveMauve on command line on bunch of gbk files. Mauve itself runs fine and I do see t…
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First of all, you should use "tag.healthy" and "methods" instead of "tag.health" and "method". Also, optimal.cutpoints() wants X to be eit…
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Past thread: https://www.biostars.org/p/178266/
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