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182 results • Page
4 of 4
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Views
Votes
Replies
0
votes
0
replies
122
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
2 days ago by
Samantha
• 0
0
votes
0
replies
120
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
2 days ago by
jain72744
▴ 10
0
votes
0
replies
120
views
How to implement an IGV to streamlit app?
python
streamlit
igv
6 days ago by
avigail.shnaider
• 0
0
votes
0
replies
118
views
News:
Online course: Introduction to Deep Learning
Python
Deep-Learning
Convolutional-Neural-Network
Machine-Learning
updated 3 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
117
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 1 day ago by
Ram
43k • written 2 days ago by
naomiboldon
• 0
0
votes
0
replies
116
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 6 days ago by
Ram
43k • written 6 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
116
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
4 days ago by
Omics data mining
▴ 260
0
votes
0
replies
115
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
3 days ago by
asalimih
▴ 60
0
votes
0
replies
114
views
Cox Model with interaction item interpretation
Cox
6 days ago by
Bine
▴ 60
0
votes
0
replies
114
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
2 days ago by
singcell
• 0
0
votes
0
replies
113
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
3 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
112
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
5 days ago by
Scott McKay
▴ 30
0
votes
0
replies
111
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
111
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
updated 1 day ago by
GenoMax
142k • written 10 days ago by
meck
• 0
0
votes
0
replies
110
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 3 days ago by
Ram
43k • written 3 days ago by
curious_butterfly
• 0
0
votes
2
replies
108
views
Output file of satools flagstat empty
samtools-flagstat
updated 5 hours ago by
Mathew
▴ 100 • written 6 hours ago by
ramendra.sarma
• 0
0
votes
0
replies
108
views
Imputation of missing genotypes
panel
beagle
imputation
5 days ago by
analyst
▴ 50
0
votes
0
replies
105
views
vdjtools
vdjtools
6 days ago by
yueli7
▴ 250
0
votes
0
replies
104
views
Cellphonedb results
cpdb
visulization
cellphonedb
5 days ago by
piotto
▴ 20
0
votes
0
replies
102
views
meffil.snp.concordance
meffil
methylation
snp_concordance
4 days ago by
kyj222637
• 0
0
votes
0
replies
101
views
Normalizing AMR gene count data
abundance
RGI
updated 6 days ago by
Ram
43k • written 6 days ago by
arshad1292
▴ 100
0
votes
0
replies
101
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 3 days ago by
Ram
43k • written 4 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
100
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
3 days ago by
Javier
• 0
0
votes
0
replies
96
views
monocle 3-- Could not get node in small cluster
monocle3
4 days ago by
synat.keam
▴ 100
0
votes
0
replies
89
views
Blog:
Overview of Nanopore Sequencing
biotech
4 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
89
views
imputation through beagle
panel
beagle
reference
imputation
1 day ago by
analyst
▴ 50
0
votes
0
replies
86
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
4 days ago by
analyst
▴ 50
0
votes
0
replies
82
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
4 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
56
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
batch
ComBat-seq
limma
RNA-seq
removeBatchEffect
3 hours ago by
t.fortunato.asquini
• 0
0
votes
0
replies
57
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
12 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
41
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
6 hours ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
28
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
3 hours ago by
rackbersingh
• 0
182 results • Page
4 of 4
Recent Votes
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
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Recent Awards •
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Scholar
to
colindaven
6.4k
Scholar
to
pjb39
▴ 200
Popular Question
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Jen
▴ 70
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Pierre Lindenbaum
161k
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Michael
54k
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Kai_Qi
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pramach1
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Recent Replies
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the R verison you are using (or packages it depends on) are not compatible with the R version you are using any…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
by
BioinfGuru
★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
Comment: Output file of satools flagstat empty
by
GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=0,Type=Flag,…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria
by
Ruqaiya
• 0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> Still, I can't understand the Invalid tag name: "1000gALT" the following line is missing in the VCF header: ##INFO=<ID=1000gALT,Num…
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